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 gmx-users@gromacs.org 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