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).
-Justin
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 <gmelaug...@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@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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