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? 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? Read http://www.gromacs.org/Support/Mailing_Lists
