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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