[gmx-users] restraints on water oxygen atoms

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Jun 11 08:05:23 CEST 2013

These are the all commands to do iteration:
After generating topology 
-    concatenate the protein and bilayer structure files:
     #cat dimer-newbox.gro popc-whole.gro > system.gro
      ( Remove unnecessary lines and update the second line of the coordinate file (total number of atoms) accordingly )

-    Use a very strong position-restraining force on protein heavy atoms to ensure that the position of the protein does not change during EM :
     Adding these lines to topology file:
     ; Strong position restraints for InflateGRO
     #include "topol_Protein_A.itp"
     #ifdef POSRE
     #include "strong_posre.itp"
     #include "topol_Protein_B.itp"
     #ifdef POSRE
     #include "strong_posre.itp"

-    Now, generate this new position restraint file using genrestr:
     #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 100000 100000 100000

-    In the .mdp file used for the minimizations, add a line "define = -DSTRONG_POSRES" to make use of these new position restraints.

-    Scale the lipid positions by a factor of 4:
     #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat

      Updating the .top file and adding POPC 238 to it.
     Energy minimization with restrained protein
     #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
     #mdrun -deffnm em

  Steepest Descents converged to Fmax < 1000 in 137 steps
Steepest Descents converged to Fmax < 100 in 4998 steps
Potential Energy  =  1.1410846e+04
Maximum force     =  9.4570084e+01 on atom 8800
Norm of force     =  3.2672191e+00

     scale down the lipids by a factor of 0.95
     #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat

    #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr
    # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 area_shrink2.dat

    # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr
    # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 area_shrink3.dat

Then, after 32 iterations, the APL reaches the value of 10% higher than the experimental value. So, I use the last gro file em_shrink32.gro as the initial configuration to solvate and next steps. But when I check the overlaps in  em_shrink32.gro, there are many improper overlaps and acyl penetration to the protein, disgusting! 


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, June 10, 2013 11:12 PM
Subject: Re: [gmx-users] restraints on water oxygen atoms

On 6/10/13 12:24 PM, Shima Arasteh wrote:
> Would you please tell me which initial deletion radius?

It would be easier for you to provide the exact command(s) you're using.  Maybe 
you've posted this information before, but this thread (or at least, related 
topics) has gone on for a very long time and maybe I'm forgetting.

> And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly?

A larger shrinking factor, e.g. 0.95 or 0.97, will shrink more slowly.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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