[gmx-users] Merging different topology files

Momin Ahmad momin.ahmad at kit.edu
Fri Sep 8 16:20:02 CEST 2017

Hi Justin,

could you provide me a link to some tutorials that focus more on the 
program structure than on the results of simulations? I did some protein 
simulation tutorials that did not really help me in understanding the 
software itself. Big thanks in advance.


Am 08.09.2017 um 13:42 schrieb Justin Lemkul:
> 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:
> [molecules]
> 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.
> -Justin
>> 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

Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu

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