Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms?
Thanks for your suggestions. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, March 25, 2013 10:22 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:50 PM, Shima Arasteh wrote: > Yes sir! > > What I have in my top file is : > ; Include forcefield parameters > #include "./charmm36-modified.ff/forcefield.itp" > > > ; Include chain topologies > #include "topol_Protein_chain_A.itp" > #ifdef POSRES > #include "protein_chain_A_posre.itp" > #endif > #include "topol_Protein_chain_B.itp" > #ifdef POSRES > #include "protein_chain_B_posre.itp" > #endif > > ; Include POPC chain topology > #include "popc.itp" > #ifdef POSRES_LIPID > #include "lipid_posre.itp" > #endif > > ; Include water topology > #include "./charmm36-modified.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "./charmm36-modified.ff/ions.itp" > > [ system ] > ; Name > Protein > > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_B 1 > POPC 238 > SOL 18706 > NA 615 > CL 617 > > > I used genrestr to create the itp file of P atom types.The generated itp file > is lipid_posre.itp. If I need to send any other information please let me > know. > In that case, lipid_posre.itp should have only one line. If you've made an index group of multiple P atoms across multiple molecules, that is the incorrect approach. Consult the manual, website, and numerous threads in the archive. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists