[gmx-users] position restraint on crystal waters

David spoel at xray.bmc.uu.se
Wed Jul 13 07:47:49 CEST 2005

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 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

More information about the gromacs.org_gmx-users mailing list