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

[Shima Arasteh]

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? 

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
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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
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