[gmx-users] position restraint

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Aug 22 15:01:48 CEST 2013

But the part in which the ions are introduced is #include "./charmm36-modified.ff/ions.itp" ,
Is this not the right place to write the posre_ion lines? As I see it is in agreement with  "Atom index n in position_restraints out of bounds" link.
So what would be the solution? I don't see any itp file generated by pdb2gmx, for the ions such as chain A  and other moleculetypes ?

Would you give me a hint and help me with it please?


---------- Forwarded message ----------
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT)
Subject: [gmx-users] position restraint
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


I want to put position restraint on an ion ,

First made an .itp file of the ion: posre_ion.itp

Then added these line to top file:
#include "./charmm36-modified.ff/ions.itp"
#include "ion_posre.itp"

And added the line to mdp file

define         = -DPOSRES_ION

But the grompp failed because it gives me the fatal error that the
include line is not in the correct position.

Would you please let me know if the inclusion of posre_ion.itp is not
as I did? What's the problem?

Thanks in advance for your suggesions.

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