[gmx-users] Merging different topology files
momin.ahmad at kit.edu
Fri Sep 8 16:20:02 CEST 2017
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
> 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.
>> 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
>>> 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.
Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu
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