[gmx-users] position restraint on crystal waters

Dilraj Lama dennis at iitk.ac.in
Wed Jul 13 16:41:26 CEST 2005

Hello David,
             Thanks for your promt reply.But i have not so well understood how to do that.I want
to apply positions restrain only for selected crystal water molecules not for all.

             So as you suggested I ran pdb2gmx and then renamed SOL to SOLA in the end of the
*.top file generated. I also copied spc.itp file in my working directory and changed
molecule name SOL to SOLA and renamed the spc.itp file as spcA.itp.I also renamed all
the HOH residues (crystal water) in *.gro file (produced by pdb2gmx) to SOLA before
running the editconf.

            I also included this spcA.itp file in *.top file.then i ran the editconf & genbox
program both works fine.but when i tried to run grompp program i got same error
"Atom index (2042) in position_restraints out of bounds (1-2014)".

            I also tried supplying the default index file to "grompp" program having a seperate
group for crystal water ( with name SOLA).But this also produced the same error.

can you pointout my mistake where i am going wrong.


> On Wed, 2005-07-13 at 10:55 +0530, Dilraj Lama wrote:
>> Hello Everyone,
>>                This is my second post on the same topic.I posted the query last week but  no one
>> has responded.Any suggestion or thought would be of great help to me.
>>         I know this topic has been discussed several times in the mailing list but i am
>> still not very clear and as a result am not able to find any solution to my problem.
>>                   I am presently trying to do simulation of a Protein which alsohave crystal
>> waters.I don't want to remove these water molecules.so after solvation of the
>> proteinin water, my system looks like :-
>> [ molecules ]
>> ; Compound        #mols
>> Protein             1
>> SOL               123 <----Crystal Water
>> SOL             31472
>> Now i am trying to do minimization of my solvated system by applying position restraint on two
>> crystal water and two residue of the protein. but when i try to preprocess my inputfiles using
>> "grompp" program,i get the following error message:
>> "Atom index (2042) in position_restraints out of bounds (1-2014)".
> you've used the wrong atom index. presumable 2042 is a water, however
> you need to restrain atom 1 of the water.
> if you only want to restrain some of the waters you will have to make
> two solvent molecule definitions (i.e. copy spc.itp to spca.itp and
> rename the molecule to SOLA and restrain only those). Do also check
> chapter 5.
>> note:2014 is the last atom number of the protein in the ".gro" file.
>> I also tried to do the same after changing the name of crystal water from SOL to SOLA but it
>> also
>> dosen't work.
>> Any suggestions/comments are most wellcome
>> Thanks In advace.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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Dilraj Lama,
PhD Student,
c/o Dr. R. Sankararamakrishnan,
Bioinformatics and Biomolecular Simulation Lab,
Dept. of BSBE,IIT-Kanpur,
email:dennis at iitk.ac.in;dilraj2002 at yahoo.com

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