[gmx-users] position restraint on crystal water

Dilraj Lama dennis at iitk.ac.in
Fri Jul 8 09:20:23 CEST 2005

Hello Everyone,
               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

                  I am presently trying to do simulation of a Protein which also have 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 input files 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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