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
