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

[Shima Arasteh]

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 <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

========================================