Thanks for all your explanations. What I get as a conclusion is this: itp files are dependent to the numbering of aoms in molecule type directive and not any other things! Each posre.itp file created by genrestr should be in consistent with the molculetype numbering!
Sincerely, Shima ________________________________ From: Justin Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Tuesday, March 26, 2013 10:54 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh <[email protected]>wrote: > The inclusion part was edited again in original top file. I dont know why > I had written that! Sorry. > But about last itp files, which you mentioned that they are created > incorrectly, 1) I 'd like to know what itp file should be created? In my > own, I just included the chain_B.itp file with the same numbering as the > chain_A.itp file. > I don't really know what that means. You should be using the files pdb2gmx gave you, at least until you understand how all of this works. You should not have to deal with anything related to restraining the protein. Hence why I've suggested that you start over. > 2) One more thing, restraints for both chains are brought just one time in > the processed.top file? I thought after each chain, the restraints which > are included should be brought and written in processed.top file!!! > > They should. But what you showed makes no sense. Restraints can't correspond to atoms that don't exist and there should only ever be on [ position_restraints ] directive per [ moleculetype ]. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
