Fwd: Fw: Fwd: [gmx-users] position restraints

[Mark Abraham]

On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh
<shima_arasteh2001 at 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 <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at 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_arasteh2001 at 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 at 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-request at 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
>
> ========================================
>
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