Do you mean that I need to make 2 backbone_posre.itp files for 2 chains? It would not be possible because I don't see any option for seperate chains when running genrestr command.
Thanks in advance. Sincerely, Shima ________________________________ From: Mark Abraham <mark.j.abra...@gmail.com> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Saturday, March 16, 2013 2:21 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh <shima_arasteh2...@yahoo.com> wrote: As you said I changed define in mdp file to define=-DPOSRE . > >I also included backbone.itp file as this: > > >; Include chain topologies >#include "topol_Protein_chain_A.itp" >#ifdef POSRE >#include "backbone_posre.itp" > >#endif >#include "topol_Protein_chain_B.itp" >#ifdef POSRE >#include "backbone_posre.itp" >#endif > > > ; Include POPC chain topology >#include "popc.itp" > >; 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 19936 >CL 2 > >But I get this fatal error that my include part for position restraints is not >correct: >Fatal error: >[ file backbone_posre.itp, line 79 ]: >Atom index (364) in position_restraints out of bounds (1-360). >This probably means that you have inserted topology section >"position_restraints" >in a part belonging to a different molecule than you intended to. >In that case move the "position_restraints" section to the right molecule. >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors > >Would you please give me suggestions? > The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean. Mark >Thanks in advance. > >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: Saturday, March 16, 2013 12:25 AM >Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints > > > >On 3/15/13 9:43 AM, Shima Arasteh wrote: >> I also included the position restraints as follows in my top file: >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #ifdef POSRE >> #include "backbone_posre.itp" >> #include "strong_posre.itp" >> #endif >> #include "topol_Protein_chain_B.itp" >> #ifdef POSRE >> #include "strong_posre.itp" >> #include "backbone_posre.itp" >> #endif >> >> As I described earlier, I included position restraints of backbone in top >> file and also added define = -DPOSRES to minim.mdp file. But it seems that >> the position restrains have not been included. Would you please suggest me >> how I can apply position restraints effectively? >> > >It won't work because -DPOSRES doesn't trigger #ifdef POSRE. To match your >topology, what you need is -DPOSRE. It is very easy to tell when position >restraints are being applied. A position restraint energy term is written to >the .log and .edr files. If it's not there, you're not applying restraints. > >-Justin > >> Thanks in advance. >> Your suggestions would be appreciated. >> Shima >> >> >> ---------- Forwarded message ---------- >> From: Shima Arasteh <shima_arasteh2...@yahoo.com> >> Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT) >> Subject: Fw: Fwd: [gmx-users] position restraints >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> >> Dear users, >> >> >> Although I put the position restraints on backbone, I get RMSD around >> 0.2 nm. Is it usual? >> This deviation is just for a minimization step only. I' m on doubt >> about keeping the backbone in a fix secondary structure. >> I' d prefer to restraint the backbone completely. Is it possible? >> >> Thanks in advance. >> >> >> >> Restraints allow, by definition, for slight deviations. >> >> Erik >> * Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to gmx-users-requ...@gromacs.org. >> >> >> >> >> Dear gmx users, >> >> I want to use restraints on backbone of my protein to keep its secondary >> structure during minimization and equilibration steps. To do so, I >> generated backbone-restrain.itp and then included it to top file. Next, >> added define = -DPOSRES to minim.mdp file. >> After minimization, when I check the minimization output file, I saw >> that the backbone of input and output files are not exactly the same. >> Is there any step which I have not done to set the restraints correctly? >> >> >> Thanks in advance. >> >> Sincerely, >> Shima >> > >-- >======================================== > >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? 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