[gmx-users] Help with position restrains for heterodimer system.
itaibloch at gmail.com
Tue May 24 12:30:40 CEST 2005
Thank you Xavier for your reply,
However, This is exactly how I did it:
I have protein_X.itp and protein_Z.itp defined in the
"whole_system.top" file --> in each of these monomers '.itp' files I
included (without "if" conditioning) the corresponding position
restrains file with the command:
(The order of including is consistent in all files).
I didn't get the last part in your reply about the numbering thing??
Is there a mistake that I'm missing here?
On 5/24/05, Xavier Periole <x.periole at rug.nl> wrote:
> itai bloch wrote:
> >Hi everyone,
> >I am trying to simulate a bilayer system with a heterodimer inside it.
> >I have a problem with the position restrained stage:
> >For some reason, only one of the two peptide chains remains fixed.
> >I have noticed that the number of POSRES in the grompp output is
> >exactly twice the number of my restrained heavy atoms (the total of
> >both peptide chains).
> >I have searched the GMX mailing list and tried the suggested solutions
> >(i.e. ordering the molecules differently and several different
> >'#include' locations), but it failed.
> You need to define the posres for each molecule and thus get two files
> posres_A.itp and posres_B.itp, they should be the same actually. Then
> each of them in the topology of each monomer.
> You have one topol.top where you include topol_A.itp and topol._B.itp.
> In each topol_?.itp you define the topology of the monomer and then put
> the posres thing, like:
> #ifdef POSRES
> #include "posre_?.itp"
> Each posres file should be defined with the numbering of the monomer alone.
> (numbering begings by 1).
> Xavier Periole - Ph.D.
> Dept. of Biophysical Chemistry / MD Group
> Univ. of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
> Tel: +31-503634329
> Fax: +31-503634800
> email: x.periole at rug.nl
> web-page: http://md.chem.rug.nl/~periole
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