If you read the documentation for genpr, it tells you that it will only generate a position restraint file for the first molecule, so grompp is telling you that only the protein is being restrained, which is what you should expect. If you really insist on restraining the water molecules, try reading about the freezegrps options for your .mdp file, but doing so will typically cause problems if you are using pressure coupling.
-Justin Quoting pragya chohan <[EMAIL PROTECTED]>: > > 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 Ideasso new they havent > even been officially released yet. > http://www.msnspecials.in/windowslive/_______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
