[gmx-users] position restraint on crystal waters

[David van der Spoel]

On Wed, 2005-07-13 at 20:11 +0530, Dilraj Lama wrote:
> 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
> message:
> "Atom index (2042) in position_restraints out of bounds (1-2014)".
atom index should be 1-2014 for protein
or 1 for water

take care that you put the [ position_restraints ] section in the right
place (i.e. in the spcA.itp file).

> 
>             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.
> 
> thanks.
> 
> > 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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> 
-- 
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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