there's also an executable topology merger available written in python
called "gromacs_topology_merger.py" as part of a the software package
"ZIBMolPy" designed for conformational analysis at
https://github.com/CMD-at-ZIB/ZIBMolPy
given (in the same directory) a topology file "topol.top" (argument 1)
and two (or more) itp files "mol1.itp" and "mol2.itp" included in the
top file, the tool writes out a new topology file (argument 2) merging
the first two molecules from the include sequence of which itp files are
given.
note: the number of molecules to be merged should be 1 in the [
molecules ] section. if one of them is meant to appear multiple times in
the merged topology, the process needs to be repeated accordingly.
vedat
Am 18.12.2012 09:38, schrieb Erik Marklund:
18 dec 2012 kl. 09.30 skrev Tsjerk Wassenaar:
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.
In principle you could use grompp for checking that. It would print out a heap
of warinngs/notes/errors if structure file and topology don't match.
Erik
Cheers,
Tsjerk
On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen <kieuthu2...@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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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
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