[gmx-users] topology file for two molecules

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 28 12:38:44 CEST 2010

Gavin Melaugh wrote:
> Hi Mark.
> I have looked this up, but I am a little uncertain. Does one of the
> topologies have to be included within the other as an .itp file. If so

No.  You #include .itp files to simply add molecules within a .top; it would be 
very rare to #include an .itp within an .itp (although it can be done).  For 
your case, your .top is simple:

#include (force field)

#include "cage.itp"
#include "pentane.itp"

[ system ]
My system

[ molecules ]
Cage    1
Pentane 1

> do I only define the [defaults directive] in the .top file i.e. I take
> it I don't include this directive in the .itp file as well.

The [defaults] directive is provided by whatever force field you #include.  If 
you're using some custom parameters, then it needs to be defined once (and only 
once) at the top of your .top file.  Otherwise, you'll get fatal errors from grompp.


> Cheers
> Gavin
> Mark Abraham wrote:
>> Look up the include file mechanism on the webpage.
>> Mark
>> ----- Original Message -----
>> From: Gavin Melaugh <gmelaugh01 at qub.ac.uk>
>> Date: Tuesday, September 28, 2010 19:04
>> Subject: [gmx-users] topology file for two molecules
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Hi all
>>> I want to run a simulation of one tert-pentane molecule inside one
>>> organic cage molecule. I have the topology files for both
>>> molecules but
>>> obviously I only need one .top file as the input for grompp.
>>> What is the
>>> most convenient way of having both topologies in one file?
>>> Many Thanks
>>> Gavin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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