[gmx-users] topology file for two molecules

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 28 12:57:40 CEST 2010

Gavin Melaugh wrote:
> 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?

You only need to use an [atomtypes] directive if you're introducing new atom 
types into the force field.  I don't know if it's necessary.  I also don't know 
if these sections can be discontinuous (i.e., one section present in cage.itp, 
another in tertpentane.itp).  Try the approach I sent you and see.  If you get 
fatal errors, then you may have to assemble a single [atomtypes] directive and 
put it either in the first .itp file you #include, or before any of the 
#includes in the .top (since #include really just means "cut-and-paste the stuff 
here," it works the same).


> Gavin
> 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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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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