[gmx-users] topology file for two molecules

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Sep 28 12:51:39 CEST 2010

Hi Justin

Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?


Justin A. Lemkul wrote:
> 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.
> -Justin
>> 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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