Loading...

adun-users@gna.org

[Prev] Thread [Next]  |  [Prev] Date [Next]

Re: [Adun-users] Adun deepak kumar Thu Feb 02 01:09:20 2012

Hi,

How to switch off the initial minimization in the minimization template?

Thanks .

On Mon, Jan 16, 2012 at 12:25 PM, deepak kumar
<[EMAIL PROTECTED]>wrote:

> I am getting this error on running the simulation. I am using BFGS.
>
>
>
> 2012-01-16 12:17:23.229 AdunCore[2516] Force field Amber99SB
> 2012-01-16 12:17:23.354 AdunCore[2516] Force field Amber99SB
> 2012-01-16 12:17:23.622 AdunCore[2516] Force field GAFF
> 2012-01-16 12:17:23.787 AdunCore[2516] Stored URL is
> file://localhost/cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation2.simulation/
> GSCBufferString
> 2012-01-16 12:17:23.787 AdunCore[2516] Decode data URL
> file://localhost/cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation2.simulation/
> and path
> /cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation2.simulation/
> 2012-01-16 12:17:23.788 AdunCore[2516] Detected error at top level -
> Simulation exiting
> 2012-01-16 12:17:23.788 AdunCore[2516] Error details follow
> 2012-01-16 12:17:23.788 AdunCore[2516] Logging error from domain
> AdunCore.ErrorDomain
> 2012-01-16 12:17:23.788 AdunCore[2516] Error code 0
> 2012-01-16 12:17:23.788 AdunCore[2516] Description - Caught unexpected
> exception
> 2012-01-16 12:17:23.788 AdunCore[2516] Detail - This is probably due to a
> programming error in the program or the AdunKernel library
> 2012-01-16 12:17:23.788 AdunCore[2516] Recovery suggestion - Notify the
> adun developers supplying the log for the simulation run
>
> Processing link {simulation = SimulationOutput/Minimisation2.simulation; }
> ~
>
> ~
>
> ~
>
>
>
> Deepak.
>
>
> On Fri, Jan 13, 2012 at 4:23 PM, Michael Johnston <
> [EMAIL PROTECTED]> wrote:
>
>> Not with SCAAS - the scaas algorithm requires knowledge of how may
>> solvent molecules have been excluded from the solvent sphere by the protein
>> and currently it gets this from the container.
>>
>> However in principal as long as the explicit solvent datasource is a
>> sphere with the correct 'hole' for the protein it would be straightforward
>> enough to estimate how many waters were removed.
>>
>> Also if you have only a few explicit waters you can treat them as
>> 'solute' and run with them in a separate system.
>>
>>
>> On Fri, Jan 13, 2012 at 2:17 PM, deepak kumar <[EMAIL PROTECTED]
>> > wrote:
>>
>>> Is it possible to use explicit solvent datasource in place of "container"
>>> in the explicit template?
>>>
>>> On Thu, Jan 12, 2012 at 5:32 PM, deepak kumar <
>>> [EMAIL PROTECTED]>wrote:
>>>
>>> > Hi
>>> >
>>> > I ran simulation without explicit solvent, used steepestdescent and
>>> BFGS
>>> > minimization. The result contains only simulation results of
>>> > steepestdescent and the system but missing BFGS simulation result.
>>> Also.,
>>> > there is error in the Aduncore.error file :
>>> >
>>> > 012-01-12 14:32:45.358 AdunCore[4941] External {}
>>> > 2012-01-12 14:32:45.392 AdunCore[4941] Build dict contains {solute =
>>> > "Name: 2kxn_with_RNA system
>>> > Number Of Atoms 196
>>> >
>>> > Interaction Types:
>>> >
>>> > Category Bonded:
>>> >         HarmonicImproperTorsion         2
>>> >          1-4Interaction       487
>>> >            HarmonicBond       212
>>> >           HarmonicAngle       375
>>> >          FourierTorsion       794
>>> >
>>> > Category Nonbonded:
>>> >         TypeTwoVDWInteraction
>>> >         CoulombElectrostatic
>>> >
>>> > There are 18036 nonbonded pairs
>>> > "; }
>>> > 2012-01-12 14:32:45.397 AdunCore[4941] Force field Amber99SB
>>> > 2012-01-12 14:32:45.627 AdunCore[4941] Arena : 5.621094 MB. Hblks :
>>> > 34.148438 MB. Uordblocks 3.685089 MB. Fordblocks 1.936005 MB
>>> > 2012-01-12 14:32:45.951 AdunCore[4941] Arena : 9.156250 MB. Hblks :
>>> > 34.148438 MB. Uordblocks 8.918381 MB. Fordblocks 0.237869 MB
>>> > 2012-01-12 14:32:46.103 AdunCore[4941] Arena : 9.671875 MB. Hblks :
>>> > 34.148438 MB. Uordblocks 9.491837 MB. Fordblocks 0.180038 MB
>>> > 2012-01-12 14:32:46.218 AdunCore[4941] Arena : 10.218750 MB. Hblks :
>>> > 34.148438 MB. Uordblocks 9.956329 MB. Fordblocks 0.262421 MB
>>> > 2012-01-12 14:32:46.372 AdunCore[4941] Arena : 13.746094 MB. Hblks :
>>> > 34.148438 MB. Uordblocks 13.302216 MB. Fordblocks 0.443878 MB
>>> > 2012-01-12 14:32:46.739 AdunCore[4941] Arena : 46.875000 MB. Hblks :
>>> > 40.761719 MB. Uordblocks 44.407532 MB. Fordblocks 2.467468 MB
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Detected error at top level -
>>> > Simulation exiting
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Error details follow
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Logging error from domain
>>> > AdunCore.ErrorDomain
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Error code 1
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Description - Controller exited
>>> > due to a known exception
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Detail - Known exceptions are
>>> > caused by common simulation problems.
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Recovery suggestion - See the
>>> > underlying error for recovery information.
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Underlying error present -
>>> Details
>>> > follow:
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Logging error from domain
>>> > AdunKernel.ErrorDomain
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Error code 3
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Description - Simulation
>>> exceeded
>>> > cell space
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Detail - This indicates an
>>> > exploding simulation.
>>> > 2012-01-12 14:32:46.756 AdunCore[4941] Recovery suggestion - Try
>>> > minimising a previous checkpoint and restarting the calculation
>>> > 2012-01-12 14:32:46.816 AdunCore[4941] Detected error at top level -
>>> > Simulation exiting
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Error details follow
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Logging error from domain
>>> > AdunCore.ErrorDomain
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Error code 1
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Description - Controller exited
>>> > due to a known exception
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Detail - Known exceptions are
>>> > caused by common simulation problems.
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Recovery suggestion - See the
>>> > underlying error for recovery information.
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Underlying error present -
>>> Details
>>> > follow:
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Logging error from domain
>>> > AdunKernel.ErrorDomain
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Error code 3
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Description - Simulation
>>> exceeded
>>> > cell space
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Detail - This indicates an
>>> > exploding simulation.
>>> > 2012-01-12 14:32:46.817 AdunCore[4941] Recovery suggestion - Try
>>> > minimising a previous checkpoint and restarting the calculation
>>> >
>>> > Processing link {simulation =
>>> SimulationOutput/Minimisation2.simulation; }
>>> > ~
>>> >
>>> > ~
>>> >
>>> > Could you tel where a i getting wrong?
>>> >
>>> > cheers.
>>> >
>>> > On Thu, Jan 12, 2012 at 10:50 AM, Michael Johnston <
>>> > [EMAIL PROTECTED]> wrote:
>>> >
>>> >> btw if you haven't done so you can check the bonds being made via
>>> >> SystemAnalysis plugin or the DataSourceDump.st script.
>>> >>
>>> >>
>>> >> On Wed, Jan 11, 2012 at 6:23 PM, Michael Johnston <
>>> >> [EMAIL PROTECTED]> wrote:
>>> >>
>>> >>>
>>> >>>
>>> >>> On Wed, Jan 11, 2012 at 6:18 PM, Nils Jan Daniel Drechsel <
>>> >>> [EMAIL PROTECTED]> wrote:
>>> >>>
>>> >>>> I deleted the
>>> >>>>
>>> >>>> <externalconnection atomindex="0" direction="In">
>>> >>>> </externalconnection>
>>> >>>> <externalconnection atomindex="0" direction="Out">
>>> >>>> </externalconnection>
>>> >>>>
>>> >>>
>>> >>> Well this specifies no connection so I don't know how the bond is
>>> being
>>> >>> added between molecules
>>> >>>
>>> >>>
>>> >>>>
>>> >>>> section from the Topology.ffml. Still, Adun is trying to make a bond
>>> >>>> between two water molecules. Even though the neglection of the
>>> torsions is
>>> >>>> actually a good thing (because we don't want these), there would
>>> still be
>>> >>>> unfavorable angles and bonds be created between the water molecules
>>> (so
>>> >>>> that they'd form a chain).
>>> >>>>
>>> >>>
>>> >>> Just to clarify the torsions neglected are those within one molecule
>>> NOT
>>> >>> between molecules.
>>> >>>
>>> >>> Are you sure the molecules are being chained together? How did you
>>> >>> determine this?
>>> >>>
>>> >>>
>>> >>>>
>>> >>>> the problem with the HETATMs is the following:
>>> >>>> We put TP3 molecules into a pdb file, all were called HETATM, there
>>> >>>> were no other molecules in the pdb. Even before starting the build
>>> process,
>>> >>>> AdunShell returned the error:
>>> >>>>
>>> >>>> Caught exception NSInvalidArgumentException
>>> >>>> Reason Index too high
>>> >>>>
>>> >>>
>>> >>> As a mentioned previously this could be just to do with internal
>>> script
>>> >>> settings - does it work in the GUI? If it does then it is just a
>>> script
>>> >>> problem, if it doesn't then we have to look elsewhere.
>>> >>>
>>> >>>
>>> >>>>
>>> >>>> On Wed, Jan 11, 2012 at 7:00 PM, Michael Johnston <
>>> >>>> [EMAIL PROTECTED]> wrote:
>>> >>>>
>>> >>>>> Actually didn't see the previous messages in this chain - I was
>>> >>>>> wondering
>>> >>>>> why the pdb file did not match the output of the builder
>>> >>>>>
>>> >>>>> The problem you mention with HETATM shouldn't occur - there is no
>>> >>>>> limit on
>>> >>>>> them - can you give more details?
>>> >>>>> It may be you have to manipulate the option dictionary in the
>>> >>>>> Builder.st
>>> >>>>> script to include the HETATMS - try from the interface to see if it
>>> >>>>> works
>>> >>>>>
>>> >>>>> On Wed, Jan 11, 2012 at 5:56 PM, Michael Johnston <
>>> >>>>> [EMAIL PROTECTED]> wrote:
>>> >>>>>
>>> >>>>> > Its not really an error ...
>>> >>>>> >
>>> >>>>> > What is happening is that the topology entry for Water in Amber
>>> >>>>> probably
>>> >>>>> > places a bond between the two hydrogens.
>>> >>>>> > This leads to Adun finding a number of fictitious torsions (since
>>> >>>>> when
>>> >>>>> > searching for torsions it doesn't account for very short loops
>>> where
>>> >>>>> the
>>> >>>>> > torsion could include the same element twice).
>>> >>>>> > However it then ignores these torsions since it can't find any
>>> >>>>> parameters
>>> >>>>> > for them in the force-field.
>>> >>>>> >
>>> >>>>> > The output is just advising you of what it has done since in
>>> other
>>> >>>>> cases
>>> >>>>> > it could be the torsions are real and the force-field has to be
>>> >>>>> extended
>>> >>>>> > with extra parameters.
>>> >>>>> >
>>> >>>>> >
>>> >>>>> > On Wed, Jan 11, 2012 at 3:50 PM, deepak kumar <
>>> >>>>> [EMAIL PROTECTED]>wrote:
>>> >>>>> >
>>> >>>>> >> Hi,
>>> >>>>> >>
>>> >>>>> >> I am trying to create a system for water but i get this error
>>> when
>>> >>>>> running
>>> >>>>> >> AdunShell :
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> the file is :
>>> >>>>> >>
>>> >>>>> >> HEADER    none                                    11-JAN-12
>>> 1UNK
>>> >>>>> >> EXPDTA    UNKNOWN
>>> >>>>> >> REMARK   2
>>> >>>>> >> REMARK   2 RESOLUTION. NOT APPLICABLE.
>>> >>>>> >> REMARK   4
>>> >>>>> >> REMARK   4 1UNK COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
>>> >>>>> >> CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1
>>> >>>>>   1
>>> >>>>> >> ATOM      1  O   HOH A   0      -4.489   4.539 -13.431  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM      2  H1  HOH A   0      -5.121   4.388 -14.181  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM      3  H2  HOH A   0      -4.029   3.669 -13.290  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM      4  O   HOH A   1      10.521  -4.473 -10.412  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM      5  H1  HOH A   1      10.131  -5.362 -10.487  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM      6  H2  HOH A   1      11.064  -4.462  -9.583  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM      7  O   HOH A   2      13.496  13.543   4.553  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM      8  H1  HOH A   2      12.701  12.989   4.690  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM      9  H2  HOH A   2      13.436  13.935   3.653  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     10  O   HOH A   3       1.503  13.548  -4.451  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     11  H1  HOH A   3       1.223  13.014  -5.209  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     12  H2  HOH A   3       1.399  14.513  -4.712  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     13  O   HOH A   4      -1.501 -19.456  -1.421  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     14  H1  HOH A   4      -1.724 -19.088  -0.514  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     15  H2  HOH A   4      -1.998 -20.307  -1.481  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     16  O   HOH A   5      -4.495   1.566   7.597  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     17  H1  HOH A   5      -5.203   2.112   7.140  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     18  H2  HOH A   5      -4.552   1.797   8.525  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     19  O   HOH A   6      10.510  13.542   1.599  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     20  H1  HOH A   6       9.709  12.952   1.634  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     21  H2  HOH A   6      10.513  14.047   2.450  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     22  O   HOH A   7      -1.514  10.560 -16.427  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     23  H1  HOH A   7      -2.288  10.568 -17.030  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     24  H2  HOH A   7      -1.818  10.920 -15.552  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     25  O   HOH A   8     -10.506   4.539  13.597  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     26  H1  HOH A   8     -11.107   3.792  13.372  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     27  H2  HOH A   8     -10.400   4.539  14.573  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     28  O   HOH A   9      -1.468 -13.430  -4.403  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     29  H1  HOH A   9      -0.623 -12.942  -4.445  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     30  H2  HOH A   9      -1.623 -13.650  -3.462  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     31  O   HOH A  10     -10.504 -13.436  -1.413  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     32  H1  HOH A  10     -10.215 -13.122  -0.513  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     33  H2  HOH A  10     -11.471 -13.562  -1.357  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     34  O   HOH A  11       1.512  13.530  13.551  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     35  H1  HOH A  11       1.549  13.533  12.575  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     36  H2  HOH A  11       1.296  12.605  13.835  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     37  O   HOH A  12     -13.499  10.546   1.585  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     38  H1  HOH A  12     -14.456  10.801   1.624  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     39  H2  HOH A  12     -13.377   9.855   2.293  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     40  O   HOH A  13      13.530   1.555 -13.417  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     41  H1  HOH A  13      14.475   1.499 -13.722  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     42  H2  HOH A  13      13.537   2.242 -12.686  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     43  O   HOH A  14     -10.489  -7.441 -10.453  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     44  H1  HOH A  14     -11.334  -7.264 -10.925  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     45  H2  HOH A  14      -9.757  -7.200 -11.067  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     46  O   HOH A  15       4.518 -13.463  10.585  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >> ATOM     47  H1  HOH A  15       4.407 -14.440  10.476  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     48  H2  HOH A  15       5.173 -13.352  11.331  1.00
>>> >>>>> >> 0.00           H
>>> >>>>> >> ATOM     49  O   HOH A  16       4.529   4.534  -4.403  1.00
>>> >>>>> >> 0.00           O
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> the error is :
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> [EMAIL PROTECTED] deepak]$ AdunShell -Script
>>> >>>>> >> /cbbl/soft/adun/Adun/Scripts/Builder.st
>>> >>>>> >> H2O_2kxn_with_RNA_without_minimization_few.pdb Amber99SB
>>> >>>>> >> 2012-01-11 16:38:33.330 AdunShell[7556] Register known
>>> languages...
>>> >>>>> >> 2012-01-11 16:38:33.335 AdunShell[7556] Language paths
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>>
>>> ("/cbbl/soft/adun/sharedhome/GNUstep/Library/StepTalk/Languages/Smalltalk.stlanguage")
>>> >>>>> >> 2012-01-11 16:38:33.350 AdunShell[7556] Caught exception
>>> >>>>> >> NSInvalidArgumentException
>>> >>>>> >> Reason Index too high.
>>> >>>>> >> [EMAIL PROTECTED] deepak]$ vi
>>> >>>>> >> H2O_2kxn_with_RNA_without_minimization_few.pdb
>>> >>>>> >> [EMAIL PROTECTED] deepak]$ AdunShell -Script
>>> >>>>> >> /cbbl/soft/adun/Adun/Scripts/Builder.st
>>> >>>>> >> H2O_2kxn_with_RNA_without_minimization_few.pdb Amber99SB
>>> >>>>> >> 2012-01-11 16:41:15.328 AdunShell[7622] Register known
>>> languages...
>>> >>>>> >> 2012-01-11 16:41:15.332 AdunShell[7622] Language paths
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>>
>>> ("/cbbl/soft/adun/sharedhome/GNUstep/Library/StepTalk/Languages/Smalltalk.stlanguage")
>>> >>>>> >> Modifing structure for Charmm
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> Done
>>> >>>>> >>
>>> >>>>> >> Information
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> Configuration File: temp.pdb
>>> >>>>> >> Selected Chains - Chain A, Chain A
>>> >>>>> >>
>>> >>>>> >> Processing Chain A
>>> >>>>> >>    Residues Selected
>>> >>>>> >>        Adding all available residues
>>> >>>>> >>    1 residues
>>> >>>>> >>    3 atoms
>>> >>>>> >>        Checking hydrogen naming and correcting if neccessary
>>> >>>>> >> Completed Chain A
>>> >>>>> >>
>>> >>>>> >> Completed configuration build
>>> >>>>> >>
>>> >>>>> >> Information
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> Building topology frame using Amber99SBTopology.ffml
>>> >>>>> >> Found all residues.
>>> >>>>> >> There are 3 atoms in the topology frame
>>> >>>>> >>
>>> >>>>> >> Completed topology frame build
>>> >>>>> >>
>>> >>>>> >> Information
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> Begining merge of expected topology and configuration from the
>>> >>>>> coordinates
>>> >>>>> >> file.
>>> >>>>> >> Expecting 3 atoms based on topology.
>>> >>>>> >> There are 3 atoms in the molecule file.
>>> >>>>> >> Number of atoms match. Looking good ...
>>> >>>>> >>
>>> >>>>> >> Merge completed
>>> >>>>> >>
>>> >>>>> >> 2012-01-11 16:41:18.037 AdunShell[7622] Logging error from
>>> domain
>>> >>>>> >> ULBuildErrorDomain
>>> >>>>> >> 2012-01-11 16:41:18.037 AdunShell[7622] Error code 4
>>> >>>>> >> 2012-01-11 16:41:18.037 AdunShell[7622] Description - Errors
>>> while
>>> >>>>> >> retrieving parameters for system.
>>> >>>>> >>
>>> >>>>> >> Information
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> Building interaction lists
>>> >>>>> >>    HarmonicBonds:
>>> >>>>> >>        There are 3 bonds
>>> >>>>> >>    HarmonicAngles:
>>> >>>>> >>        There are 3 angle interactions
>>> >>>>> >>    FourierTorsions:
>>> >>>>> >>        Removed 3 FourierTorsion interactions.
>>> >>>>> >> See errors.
>>> >>>>> >>        There are 3 proper torsion interactions
>>> >>>>> >>    HarmonicImproperTorsions:
>>> >>>>> >>        There are 0 improper torsion interactions
>>> >>>>> >>    Nonbonded Interactions
>>> >>>>> >>        There are 0 nonbonded interactions
>>> >>>>> >>        There are 0 1-4 interactions
>>> >>>>> >>
>>> >>>>> >> Completed interactions build
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> Errors
>>> >>>>> >>
>>> >>>>> >> Errors while retrieving parameters for system.
>>> >>>>> >>
>>> >>>>> >> The following interactions were missing paramters
>>> >>>>> >>  and have been omitted.
>>> >>>>> >>
>>> >>>>> >> Unable to find parameters for the following FourierTorsion
>>> >>>>> interactions.
>>> >>>>> >> (HW, OW, HW, HW)
>>> >>>>> >> (HW, OW, HW, HW)
>>> >>>>> >> (OW, HW, HW, OW)
>>> >>>>> >>
>>> >>>>> >> Depending on the force field these omissions may or may not be
>>> >>>>> critical.
>>> >>>>> >>
>>> >>>>> >> Finished
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> thanks.
>>> >>>>> >>
>>> >>>>> >> On Tue, Jan 10, 2012 at 2:57 PM, Michael Johnston <
>>> >>>>> >> [EMAIL PROTECTED]> wrote:
>>> >>>>> >>
>>> >>>>> >> > The link options you have specify that the initial conditions
>>> of
>>> >>>>> all the
>>> >>>>> >> > systems in the simulation should be linked to the minimisation
>>> >>>>> >> calculation
>>> >>>>> >> > - however the number of water molecules in this simulation is
>>> not
>>> >>>>> equal
>>> >>>>> >> to
>>> >>>>> >> > the number in the minimisation simulation so the link fails
>>> (see
>>> >>>>> bolded
>>> >>>>> >> > statements in the error output below).
>>> >>>>> >> >
>>> >>>>> >> > Check that the dimensions of the solvent sphere are the same
>>> in
>>> >>>>> both
>>> >>>>> >> > cases.
>>> >>>>> >> > Also check that other initial conditions (e.g. the center of
>>> mass
>>> >>>>> of the
>>> >>>>> >> > protein, the center of mass of the sphere) are the same in
>>> both
>>> >>>>> cases.
>>> >>>>> >> If
>>> >>>>> >> > they aren't then a slightly different number of water
>>> molecules
>>> >>>>> may be
>>> >>>>> >> used
>>> >>>>> >> > to fill the sphere.
>>> >>>>> >> >
>>> >>>>> >> > The AdunCore.log will tell you how everything is setup after
>>> the
>>> >>>>> >> template
>>> >>>>> >> > is processed - if you run the simulation without the link step
>>> >>>>> (just
>>> >>>>> >> for 1
>>> >>>>> >> > step) you can then compare the systems to the minimisation to
>>> see
>>> >>>>> if
>>> >>>>> >> they
>>> >>>>> >> > are identical.
>>> >>>>> >> >
>>> >>>>> >> > On Mon, Jan 9, 2012 at 6:49 PM, deepak kumar <
>>> >>>>> >> [EMAIL PROTECTED]>wrote:
>>> >>>>> >> >
>>> >>>>> >> >> Hi,
>>> >>>>> >> >>
>>> >>>>> >> >> After running the simulation on the created system I get this
>>> >>>>> >> >> Aduncore.errors file. I am using minimization template and
>>> >>>>> explicit
>>> >>>>> >> >> template.
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >> >> 2012-01-09 19:05:47.946 AdunCore[26715] Force field Amber99
>>> >>>>> >> >> 2012-01-09 19:05:48.060 AdunCore[26715] Force field Amber99
>>> >>>>> >> >> 2012-01-09 19:05:48.292 AdunCore[26715] Force field GAFF
>>> >>>>> >> >> 2012-01-09 19:05:48.499 AdunCore[26715] Encoded data path
>>> and
>>> >>>>> current
>>> >>>>> >> >> location are not equal
>>> >>>>> >> >> 2012-01-09 19:05:48.499 AdunCore[26715] Substituting stored
>>> >>>>> data path
>>> >>>>> >> >> with
>>> >>>>> >> >> current location
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >>
>>> >>>>>
>>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb_bfgs_steepdescent/SimulationOutput/Minimisation2.simulation/
>>> >>>>> >> >> 2012-01-09 19:05:48.500 AdunCore[26715] Stored URL is
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >>
>>> >>>>>
>>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb_bfgs_steepdescent/SimulationOutput/Minimisation2.simulation/
>>> >>>>> >> >> GSCBufferString
>>> >>>>> >> >> 2012-01-09 19:05:48.500 AdunCore[26715] Decode data URL
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >>
>>> >>>>>
>>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb_bfgs_steepdescent/SimulationOutput/Minimisation2.simulation/
>>> >>>>> >> >> and path
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >>
>>> >>>>>
>>> /cbbl/users/deepak/simulations/mac_2rrb_bfgs_steepdescent/SimulationOutput/Minimisation2.simulation/
>>> >>>>> >> >> 2012-01-09 19:05:49.860 AdunCore[26715] Replaced
>>> coordinates of
>>> >>>>> system
>>> >>>>> >> >> 2rrbsystem with those from link
>>> >>>>> >> >> 2012-01-09 19:05:49.866 AdunCore[26715] Replaced velocties
>>> of
>>> >>>>> system
>>> >>>>> >> >> 2rrbsystem with those from link
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715]* Unable to set
>>> >>>>> coordinates for
>>> >>>>> >> >> H2OContainer using link*
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715] Incompatible number
>>> of
>>> >>>>> >> elements
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715] Detected error at
>>> top
>>> >>>>> level -
>>> >>>>> >> >> Simulation exiting
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715] Error details follow
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715] Logging error from
>>> >>>>> domain
>>> >>>>> >> >> AdunCore.ErrorDomain
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715] Error code 13
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715] Description -
>>> Unable to
>>> >>>>> set
>>> >>>>> >> >> coordinates for H2OContainer using link
>>> >>>>> >> >> 2012-01-09 19:05:50.099 AdunCore[26715]* Detail - The two
>>> >>>>> systems do
>>> >>>>> >> not
>>> >>>>> >> >> contain the same number of elements*
>>> >>>>> >> >> Processing link {simulation =
>>> >>>>> >> SimulationOutput/Minimisation2.simulation; }
>>> >>>>> >> >> ~
>>> >>>>> >> >>
>>> >>>>> >> >> ~
>>> >>>>> >> >> Could you let me know where is the problem.
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >> >> cheers.
>>> >>>>> >> >>
>>> >>>>> >> >> On Mon, Jan 9, 2012 at 9:48 AM, Jordi Villà i Freixa <
>>> >>>>> >> >> [EMAIL PROTECTED]> wrote:
>>> >>>>> >> >>
>>> >>>>> >> >> > good, thanks
>>> >>>>> >> >> >
>>> >>>>> >> >> > On Jan 9, 2012, at 9:19 AM, Miguel A. Sánchez Gómez wrote:
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Hi
>>> >>>>> >> >> >
>>> >>>>> >> >> > I've just taken out the computer pelargonium of the CBBL
>>> >>>>> queue. Now
>>> >>>>> >> this
>>> >>>>> >> >> > computer it is only in the 'short' queue.
>>> >>>>> >> >> >
>>> >>>>> >> >> > Miguel A. Sánchez Gómez
>>> >>>>> >> >> > System Administrator
>>> >>>>> >> >> > Research Group on Biomedical Informatics - GRIB (IMIM-UPF)
>>> >>>>> >> >> >
>>> >>>>> >> >> > Barcelona Biomedical Research Park (office 4.80)
>>> >>>>> >> >> > Doctor Aiguader 88 | 08003 Barcelona (Spain)
>>> >>>>> >> >> > Phone: +34/ 93 316 0522 | Fax: +34/ 93 3160 550
>>> >>>>> >> >> > e-mail: [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> > On 01/05/2012 08:59 PM, Jordi Villà i Freixa wrote:
>>> >>>>> >> >> >
>>> >>>>> >> >> > Miguel, Alfons, could you take pelargonium out of the CBBL
>>> >>>>> queue?
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> > Begin forwarded message:
>>> >>>>> >> >> >
>>> >>>>> >> >> >  *From: *Nils Jan Daniel Drechsel <
>>> >>>>> [EMAIL PROTECTED]>
>>> >>>>> >> >> >  *Date: *January 5, 2012 7:27:37 PM GMT+01:00
>>> >>>>> >> >> >  *To: *deepak kumar <[EMAIL PROTECTED]>
>>> >>>>> >> >> >  *Cc: [EMAIL PROTECTED]
>>> >>>>> >> >> >  *Subject: **Re: [Adun-users] Adun*
>>> >>>>> >> >> >
>>> >>>>> >> >> > this has been solved. It is due to the fact that the job
>>> was
>>> >>>>> >> executed on
>>> >>>>> >> >> > the machine pelargonium, which is running a different
>>> version
>>> >>>>> of
>>> >>>>> >> >> fedora. We
>>> >>>>> >> >> > need to take it out of the cbbl queue as adun will not run
>>> >>>>> there.
>>> >>>>> >> >> >
>>> >>>>> >> >> > On Thu, Jan 5, 2012 at 7:20 PM, deepak kumar <
>>> >>>>> >> >> [EMAIL PROTECTED]
>>> >>>>> >> >> > >wrote:
>>> >>>>> >> >> >
>>> >>>>> >> >> > Hi,
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  I ran the test simulation on Mac. Was able to create the
>>> >>>>> simulation.
>>> >>>>> >> >> when
>>> >>>>> >> >> >
>>> >>>>> >> >> > submitted it to run i got this error in the "stderr.txt"
>>> file:
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  AdunCore: error while loading shared libraries:
>>> >>>>> >> >> libbfd-2.17.50.0.18-1.so:
>>> >>>>> >> >> >
>>> >>>>> >> >> > cannot open shared object file: No such file or directory
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Could you help. attached below are the datasource and
>>> template
>>> >>>>> >> files.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  cheers.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  On Thu, Jan 5, 2012 at 11:13 AM, Jordi Villà i Freixa <
>>> >>>>> >> >> >
>>> >>>>> >> >> > [EMAIL PROTECTED]> wrote:
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  try to follow Michael's advice.
>>> >>>>> >> >> >
>>> >>>>> >> >> >  uninstall 0.26 version for gnustep-startup and install
>>> 0.25
>>> >>>>> using
>>> >>>>> >> the
>>> >>>>> >> >> >
>>> >>>>> >> >> >  same
>>> >>>>> >> >> >
>>> >>>>> >> >> >  instructions than before
>>> >>>>> >> >> http://lavandula.imim.es/adun-new/?page_id=1400
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   Begin forwarded message:
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   *From: *Michael Johnston <[EMAIL PROTECTED]>
>>> >>>>> >> >> >
>>> >>>>> >> >> >  *Date: *January 5, 2012 11:00:54 AM GMT+01:00
>>> >>>>> >> >> >
>>> >>>>> >> >> >  *To: *César Ávila <[EMAIL PROTECTED]>
>>> >>>>> >> >> >
>>> >>>>> >> >> >  *Cc: *Jordi Villà i Freixa <[EMAIL PROTECTED]>,
>>> >>>>> >> >> >
>>> >>>>> >> >> >  [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >  *Subject: **Re: [Adun-users] Adun*
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   The last gnustep-startup that worked reliably for me was
>>> >>>>> 0.25 - I
>>> >>>>> >> use
>>> >>>>> >> >> >
>>> >>>>> >> >> >  this
>>> >>>>> >> >> >
>>> >>>>> >> >> >  to build the packages for Fedora/Suse and these worked
>>> >>>>> normally
>>> >>>>> >> when I
>>> >>>>> >> >> >
>>> >>>>> >> >> >  tested them. As Cesar mentioned use the guidelines on this
>>> >>>>> page -
>>> >>>>> >> >> >
>>> >>>>> >> >> >  http://lavandula.imim.es/adun-new/?page_id=186 - to work
>>> out
>>> >>>>> what
>>> >>>>> >> >> >
>>> >>>>> >> >> >  gnustep
>>> >>>>> >> >> >
>>> >>>>> >> >> >  library versions to use.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   Post this sartup versionthere are a number of changes in
>>> >>>>> gnustep to
>>> >>>>> >> >> >
>>> >>>>> >> >> >  support the apples new objective-c runtime (OSX 10.5
>>> >>>>> compatible) the
>>> >>>>> >> >> >
>>> >>>>> >> >> >  effect
>>> >>>>> >> >> >
>>> >>>>> >> >> >  of which is to break AdunShell.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   Also FYI there is some problem between the latest Cairo
>>>  (an
>>> >>>>> >> >> underlying
>>> >>>>> >> >> >
>>> >>>>> >> >> >  graphical library) on ubuntu and the latest gui which
>>> stops
>>> >>>>> the Adun
>>> >>>>> >> >> from
>>> >>>>> >> >> >
>>> >>>>> >> >> >  starting (not sure if this problem exists on other
>>> distros -
>>> >>>>> the
>>> >>>>> >> fact
>>> >>>>> >> >> >
>>> >>>>> >> >> >  that
>>> >>>>> >> >> >
>>> >>>>> >> >> >  the gui opens for deepak with 0.26 suggests not).
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   As Cesar said if you can send along the log files
>>> >>>>> (specifically
>>> >>>>> >> >> UL.log)
>>> >>>>> >> >> >
>>> >>>>> >> >> >  after you observe the problem we can work from there.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   2012/1/4 César Ávila <[EMAIL PROTECTED]>
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   I've seen a lot of errors with the gui using gnustep
>>> version
>>> >>>>> other
>>> >>>>> >> >> than
>>> >>>>> >> >> >
>>> >>>>> >> >> >   the
>>> >>>>> >> >> >
>>> >>>>> >> >> >   one posted in
>>> >>>>> >> >> >
>>> >>>>> >> >> >    http://lavandula.imim.es/adun-new/?page_id=186
>>> >>>>> >> >> >
>>> >>>>> >> >> >   **
>>> >>>>> >> >> >
>>> >>>>> >> >> >   I personally prefer gnustep startup 0.20.1 (it works for
>>> me).
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >    2012/1/4 Jordi Villà i Freixa <
>>> [EMAIL PROTECTED]>
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >    Deepak uses an adun version obtained following the
>>> steps in
>>> >>>>> >> >> >
>>> >>>>> >> >> >    http://lavandula.imim.es/adun-new/?page_id=1400
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >     On Jan 4, 2012, at 6:55 PM, César Ávila wrote:
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >     Hi Deepak and welcome to Adun.
>>> >>>>> >> >> >
>>> >>>>> >> >> >     As Nils mentioned, some problems might arise with the
>>> GUI
>>> >>>>> >> related to
>>> >>>>> >> >> >
>>> >>>>> >> >> >    the
>>> >>>>> >> >> >
>>> >>>>> >> >> >    GNUStep version that you have installed on your system.
>>> >>>>> >> >> >
>>> >>>>> >> >> >     Can you provide more information about this? I think it
>>> >>>>> might
>>> >>>>> >> also
>>> >>>>> >> >> >
>>> >>>>> >> >> >    come
>>> >>>>> >> >> >
>>> >>>>> >> >> >    helpful any error messages that you receive in
>>> >>>>> >> >> >
>>> >>>>> >> >> >     ~/adun/UL.log and ~/adun/AdunServer.log
>>> >>>>> >> >> >
>>> >>>>> >> >> >     Cheers
>>> >>>>> >> >> >
>>> >>>>> >> >> >     Cesar
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >      2012/1/4 Nils Jan Daniel Drechsel <
>>> >>>>> [EMAIL PROTECTED]
>>> >>>>> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >      Just to add something,
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >       Deepak is working in the linux version of the GUI.
>>> I've
>>> >>>>> never
>>> >>>>> >> had
>>> >>>>> >> >> >
>>> >>>>> >> >> >     these
>>> >>>>> >> >> >
>>> >>>>> >> >> >     problems in the mac version, so I think it might be
>>> GNUstep
>>> >>>>> >> >> >
>>> >>>>> >> >> >    related?
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >       On Wed, Jan 4, 2012 at 4:34 PM, deepak kumar <
>>> >>>>> >> >> >
>>> >>>>> >> >> >     [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >      wrote:
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >       Hi all,
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        I am a new user of Adun. While working with it I
>>> came
>>> >>>>> across
>>> >>>>> >> some
>>> >>>>> >> >> >
>>> >>>>> >> >> >       problems,
>>> >>>>> >> >> >
>>> >>>>> >> >> >       as below:
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        a) I am trying to create a system. After creating
>>> the
>>> >>>>> system
>>> >>>>> >> and
>>> >>>>> >> >> >
>>> >>>>> >> >> >     saving
>>> >>>>> >> >> >
>>> >>>>> >> >> >     it,
>>> >>>>> >> >> >
>>> >>>>> >> >> >       nothing appears at the database ([EMAIL PROTECTED])
>>> in
>>> >>>>> the
>>> >>>>> >> >> >
>>> >>>>> >> >> >     "systems" of
>>> >>>>> >> >> >
>>> >>>>> >> >> >     GUI.
>>> >>>>> >> >> >
>>> >>>>> >> >> >       b) If i try to rename the system from "none" to some
>>> >>>>> desired
>>> >>>>> >> name
>>> >>>>> >> >> >
>>> >>>>> >> >> >     the
>>> >>>>> >> >> >
>>> >>>>> >> >> >     tool
>>> >>>>> >> >> >
>>> >>>>> >> >> >       hangs and the system is not renamed. When trying to
>>> >>>>> >> remove/cut/...
>>> >>>>> >> >> >
>>> >>>>> >> >> >     use
>>> >>>>> >> >> >
>>> >>>>> >> >> >     any
>>> >>>>> >> >> >
>>> >>>>> >> >> >       of the "edit" options, it does not work.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        Could you plz let me know how can i resolve these
>>> >>>>> problems.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        cheers.
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        --
>>> >>>>> >> >> >
>>> >>>>> >> >> >       Deepak Kumar
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        Computational Biochemistry and Biophysics lab
>>> >>>>> >> >> >
>>> >>>>> >> >> >       Research Group on Biomedical Informatics (GRIB) -
>>> >>>>> IMIM/UPF
>>> >>>>> >> >> >
>>> >>>>> >> >> >       Parc de Recerca Biomèdica de Barcelona
>>> >>>>> >> >> >
>>> >>>>> >> >> >       C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        Phone: +48 66 46 82950
>>> >>>>> >> >> >
>>> >>>>> >> >> >       E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <
>>> >>>>> >> >> >
>>> >>>>> >> >> >    [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >   %20>
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >        This message has been automatically forwarded to
>>> you by
>>> >>>>> the
>>> >>>>> >> Adun
>>> >>>>> >> >> >
>>> >>>>> >> >> >     team
>>> >>>>> >> >> >
>>> >>>>> >> >> >     http://adun.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> >       _______________________________________________
>>> >>>>> >> >> >
>>> >>>>> >> >> >       Adun-users mailing list
>>> >>>>> >> >> >
>>> >>>>> >> >> >       [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >       https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >       This message has been automatically forwarded to you
>>> by
>>> >>>>> the
>>> >>>>> >> Adun
>>> >>>>> >> >> >
>>> >>>>> >> >> >    team
>>> >>>>> >> >> >
>>> >>>>> >> >> >    http://adun.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> >      _______________________________________________
>>> >>>>> >> >> >
>>> >>>>> >> >> >      Adun-users mailing list
>>> >>>>> >> >> >
>>> >>>>> >> >> >      [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >      https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >      This message has been automatically forwarded to you
>>> by
>>> >>>>> the Adun
>>> >>>>> >> >> >
>>> >>>>> >> >> >   team
>>> >>>>> >> >> >
>>> >>>>> >> >> >   http://adun.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> >     _______________________________________________
>>> >>>>> >> >> >
>>> >>>>> >> >> >     Adun-users mailing list
>>> >>>>> >> >> >
>>> >>>>> >> >> >     [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >     https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >    This message has been automatically forwarded to you by
>>> the
>>> >>>>> Adun
>>> >>>>> >> team
>>> >>>>> >> >> >
>>> >>>>> >> >> >   http://adun.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> >   _______________________________________________
>>> >>>>> >> >> >
>>> >>>>> >> >> >   Adun-users mailing list
>>> >>>>> >> >> >
>>> >>>>> >> >> >   [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >   https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >   --
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Jordi Villà i Freixa
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Computational Biochemistry and Biophysics lab
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Parc de Recerca Biomèdica de Barcelona
>>> >>>>> >> >> >
>>> >>>>> >> >> >  C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Tel: +34 93 316 0504 // Fax: +34 93 316 0550
>>> >>>>> >> >> >
>>> >>>>> >> >> >  e-mail: [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> >  http://cbbl.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  --
>>> >>>>> >> >> >
>>> >>>>> >> >> > Deepak Kumar
>>> >>>>> >> >> >
>>> >>>>> >> >> > Bioinformatics Laboratory
>>> >>>>> >> >> >
>>> >>>>> >> >> > Institute of Molecular Biology and Biotechnology
>>> >>>>> >> >> >
>>> >>>>> >> >> > Adam Mickiewicz University
>>> >>>>> >> >> >
>>> >>>>> >> >> > Umultowska 89, 61-614 Poznan, Poland
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  Phone: +48 66 46 82950
>>> >>>>> >> >> >
>>> >>>>> >> >> > E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <
>>> >>>>> [EMAIL PROTECTED]
>>> >>>>> >> >> %20><[EMAIL PROTECTED]>
>>> >>>>> >> >>
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >  This message has been automatically forwarded to you by
>>> the
>>> >>>>> Adun
>>> >>>>> >> team
>>> >>>>> >> >> >
>>> >>>>> >> >> > http://adun.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> > _______________________________________________
>>> >>>>> >> >> >
>>> >>>>> >> >> > Adun-users mailing list
>>> >>>>> >> >> >
>>> >>>>> >> >> > [EMAIL PROTECTED]
>>> >>>>> >> >> >
>>> >>>>> >> >> > https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> > This message has been automatically forwarded to you by the
>>> >>>>> Adun team
>>> >>>>> >> >> > http://adun.imim.es
>>> >>>>> >> >> > _______________________________________________
>>> >>>>> >> >> > Adun-users mailing list
>>> >>>>> >> >> > [EMAIL PROTECTED]
>>> >>>>> >> >> > https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >> > --
>>> >>>>> >> >> > Jordi Villà i Freixa
>>> >>>>> >> >> > Computational Biochemistry and Biophysics lab
>>> >>>>> >> >> > Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>>> >>>>> >> >> > Parc de Recerca Biomèdica de Barcelona
>>> >>>>> >> >> > C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>> >>>>> >> >> > Tel: +34 93 316 0504 // Fax: +34 93 316 0550
>>> >>>>> >> >> > e-mail: [EMAIL PROTECTED]
>>> >>>>> >> >> > http://cbbl.imim.es
>>> >>>>> >> >> >
>>> >>>>> >> >> >
>>> >>>>> >> >>
>>> >>>>> >> >>
>>> >>>>> >> >> --
>>> >>>>> >> >> Deepak Kumar
>>> >>>>> >> >> Bioinformatics Laboratory
>>> >>>>> >> >> Institute of Molecular Biology and Biotechnology
>>> >>>>> >> >> Adam Mickiewicz University
>>> >>>>> >> >> Umultowska 89, 61-614 Poznan, Poland
>>> >>>>> >> >>
>>> >>>>> >> >> Phone: +48 66 46 82950
>>> >>>>> >> >> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <
>>> >>>>> [EMAIL PROTECTED]
>>> >>>>> >> %20>
>>> >>>>> >> >>
>>> >>>>> >> >> This message has been automatically forwarded to you by the
>>> Adun
>>> >>>>> team
>>> >>>>> >> >> http://adun.imim.es
>>> >>>>> >> >> _______________________________________________
>>> >>>>> >> >> Adun-users mailing list
>>> >>>>> >> >> [EMAIL PROTECTED]
>>> >>>>> >> >> https://mail.gna.org/listinfo/adun-users
>>> >>>>> >> >>
>>> >>>>> >> >
>>> >>>>> >> >
>>> >>>>> >>
>>> >>>>> >>
>>> >>>>> >> --
>>> >>>>> >> Deepak Kumar
>>> >>>>> >> Bioinformatics Laboratory
>>> >>>>> >> Institute of Molecular Biology and Biotechnology
>>> >>>>> >> Adam Mickiewicz University
>>> >>>>> >> Umultowska 89, 61-614 Poznan, Poland
>>> >>>>> >>
>>> >>>>> >> Phone: +48 66 46 82950
>>> >>>>> >> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <
>>> [EMAIL PROTECTED]
>>> >>>>> %20>
>>> >>>>> >>
>>> >>>>> >> This message has been automatically forwarded to you by the Adun
>>> >>>>> team
>>> >>>>> >> http://adun.imim.es
>>> >>>>> >> _______________________________________________
>>> >>>>> >> Adun-users mailing list
>>> >>>>> >> [EMAIL PROTECTED]
>>> >>>>> >> https://mail.gna.org/listinfo/adun-users
>>> >>>>> >>
>>> >>>>> >
>>> >>>>> >
>>> >>>>>
>>> >>>>> This message has been automatically forwarded to you by the Adun
>>> team
>>> >>>>> http://adun.imim.es
>>> >>>>> _______________________________________________
>>> >>>>> Adun-users mailing list
>>> >>>>> [EMAIL PROTECTED]
>>> >>>>> https://mail.gna.org/listinfo/adun-users
>>> >>>>>
>>> >>>>
>>> >>>>
>>> >>>
>>> >>
>>> >
>>> >
>>> > --
>>> > Deepak Kumar
>>> > Bioinformatics Laboratory
>>> > Institute of Molecular Biology and Biotechnology
>>> > Adam Mickiewicz University
>>> > Umultowska 89, 61-614 Poznan, Poland
>>> >
>>> > Phone: +48 66 46 82950
>>> > E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]
>>> %20>
>>> >
>>>
>>>
>>>
>>> --
>>> Deepak Kumar
>>> Bioinformatics Laboratory
>>> Institute of Molecular Biology and Biotechnology
>>> Adam Mickiewicz University
>>> Umultowska 89, 61-614 Poznan, Poland
>>>
>>> Phone: +48 66 46 82950
>>> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>
>>>
>>> This message has been automatically forwarded to you by the Adun team
>>> http://adun.imim.es
>>> _______________________________________________
>>> Adun-users mailing list
>>> [EMAIL PROTECTED]
>>> https://mail.gna.org/listinfo/adun-users
>>>
>>
>>
>
>
> --
> Deepak Kumar
> Bioinformatics Laboratory
> Institute of Molecular Biology and Biotechnology
> Adam Mickiewicz University
> Umultowska 89, 61-614 Poznan, Poland
>
> Phone: +48 66 46 82950
> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>
>



-- 
Deepak Kumar
Bioinformatics Laboratory
Institute of Molecular Biology and Biotechnology
Adam Mickiewicz University
Umultowska 89, 61-614 Poznan, Poland

Phone: +48 66 46 82950
E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>

This message has been automatically forwarded to you by the Adun team 
http://adun.imim.es
_______________________________________________
Adun-users mailing list
[EMAIL PROTECTED]
https://mail.gna.org/listinfo/adun-users