[gmx-users] position restrain

[pragya chohan]

hi 
I have a system of protein, popc,water and Cl ions. I want to position restrain protein and water as without position restrain water is going into the membrane . So I made a group of protein and water together using make_ndx and then genpr. When i ran grompp i got the following error:

-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108

Fatal error:
[ file "posre1.itp", line 582 ]:
             Atom index (5362) in position_restraints out of bounds (1-577)

The commands i used are:
make_ndx -f em_dpt_popc.gro -o
 0 System              : 12663 atoms
  1 Protein             :   577 atoms
  2 Protein-H           :   456 atoms
  3 C-alpha             :    59 atoms
  4 Backbone            :   177 atoms
  5 MainChain           :   237 atoms
  6 MainChain+Cb        :   294 atoms
  7 MainChain+H         :   296 atoms
  8 SideChain           :   281 atoms
  9 SideChain-H         :   219 atoms
 10 Prot-Masses         :   577 atoms
 11 Non-Protein         : 12086 atoms
 12 POPC                :  4784 atoms
 13 SOL                 :  7299 atoms
 14 Cl                  :     3 atoms
 15 Other               : 12086 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit

> 1|13

Copied index group 1 'Protein'
Copied index group 13 'SOL'
Merged two groups with OR: 577 7299 -> 7876

 16 Protein_SOL         :  7876 atoms

> q

genpr -f em_dpt_popc.gro -o posre1 -n index.ndx

Group    16 ( Protein_SOL) has  7876 elements
Select a group: 16
Selected 16: 'Protein_SOL'

grompp -f pr.mdp -c em_dpt_popc.gro -n index.ndx -p dpt_popc_water.top -o pr_dpt_popc

What is the best way to do this? Please suggest.
_________________________________________________________________
Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet.
http://www.msnspecials.in/windowslive/