[gmx-users] Merging different topology files

Justin Lemkul jalemkul at vt.edu
Fri Sep 8 13:43:09 CEST 2017

On 9/8/17 5:50 AM, Momin Ahmad wrote:
> Thank you for your help. I already did that but i get a weird error 
> that i can not solve. I attached the topology files and the error 
> message. Maybe the numbering of the residues has to be changed? Thanks 
> in advance.

You have lots of missing parameters, which means your force field 
doesn't know how to represent these molecules.  You are also missing 
several bonded interactions in your ammonia topology, so the simulation 
won't be stable.  As to the last fatal error, your [molecules] directive 
doesn't actually specify how many molecules you have:


There need to be actual numbers here.  Please go back and do some basic 
GROMACS tutorials and reading in the PDF manual (particularly Chapter 5) 
to understand topology format before trying to do something like this.  
It's very easy to make lots of mistakes, some obvious and some not.


> Cheers,
> Momin
> Am 07.09.2017 um 21:08 schrieb Justin Lemkul:
>> On 9/7/17 10:19 AM, Momin Ahmad wrote:
>>> Hello all,
>>> is there a simple way to merge two or more topology files into one? 
>>> I am trying to use grompp to set up a simulation but my solvation 
>>> contains different molecules which have different .top files. I also 
>>> tried creating a main topology file which includes the other two 
>>> topologies but without success. Hope anyone knows how to solve this.
>> The #include mechanism is the only way to do this.  If you have two 
>> .top (system topology) files, then:
>> 1. Remove any #include statement for a parent force field (i.e. the 
>> file with [defaults] in it)
>> 2. Remove any [system] or [molecules] directive
>> (you now have proper .itp format)
>> 3. Remove any redundant #include statements (e.g. for water, ions) to 
>> avoid "moleculetype redefined" errors
>> 4. Construct a new .top that #includes a parent force field, your two 
>> new .itp files, and has [system] and [molecules] directives.
>> -Justin


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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