[gmx-users] merge .gro, .top files

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Dec 18 09:30:04 CET 2012

Hi KT,

If you mean concatenating frames in .gro files, you can use trjcat or just
cat. If you mean merging the coordinates, it's a wee bit more complicated.
Since you also ask for top files, I guess that's the case. Here's a snippet
of python code that will do the trick:

#!/usr/bin/env python

import sys

f = [open(i).readlines() for i in sys.argv[1:]]
print "Merged gro file\n%5d" % (sum([len(i) for i in f]) - 3*len(f))
print "".join(["".join(i[2:-1]) for i in f]),
print f[0][-1]

For the top files, it is necessary to ensure all the moleculetypes are
#included, and that the [ molecules ] listing under [ system ] has the
right number and order of the molecules in the merged gro file. There's no
tool for that that I know of.



On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com>wrote:

> Dear All,
> I don't know which tools used to merge 2 files .gro, 2 files .top ?
> Can i use trjcat ?
> Thanks !
> KT
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4

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