Thanks for your help. My simulation ran with your idea. ---------------------------------------- > Date: Thu, 15 Nov 2007 13:34:40 -0500 > From: [EMAIL PROTECTED] > To: [email protected] > Subject: Re: [gmx-users] position restrain > > 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 Ideas—so new they haven’t > > 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
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