[gmx-users] Merging different topology files
jalemkul at vt.edu
Thu Sep 7 21:09:04 CEST 2017
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 A. Lemkul, Ph.D.
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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