[gmx-users] position restrained minimization on the one part of a system

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 27 06:58:57 CEST 2011

Hi Atila,

> ; Include chain topologies
> #include "complex_Protein_chain_A.itp"
> #include "complex_DNA_chain_B.itp"
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_B.itp"

Aside from the missing #ifdefs that Mark mentioned, this is also
plainly wrong. The position restraints are part of the molecule
definition, so now both sets of restraints are made part of the last
moleculetype, which is the DNA chain. You'll have to have

; Include chain topologies
#include "complex_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"

#include "complex_DNA_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"

I note that the position restraints for chain B are called protein too...



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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