[gmx-users] position restraint on crystal waters

Dilraj Lama dennis at iitk.ac.in
Wed Jul 13 07:25:27 CEST 2005

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)".

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.
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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