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
--
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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