On 12/26/12 7:46 PM, Kieu Thu Nguyen wrote:
Do you mean that i have to add the line "sed '2s/^.*$/'$(wc -l file.gro)'/'
file.gro > out.gro" into the old script merge.py ?
sed is a standard *nix command, issued from the command line.
-Justin
On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
Hi KT,
To update the number of atoms in a merged .gro file, assuming a single
frame and no empty lines after the box definition, you have to replace the
second line with the number of lines minus three:
sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro > out.gro
Cheers,
Tsjerk
On Tue, Dec 25, 2012 at 7:33 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com
wrote:
But i don't see file "gromacs_topology_merger.py" in the web Vedat gave
me.
Tsjerk, can you give me the script for updating the number of atoms ? I
searched in google, but i have not found it yet. It's really my stupid
question, but i don't know why.
Thanks !
Best regards,
KT
On Tue, Dec 18, 2012 at 6:43 PM, Kieu Thu Nguyen <kieuthu2...@gmail.com
wrote:
thank all so much :-)
KT
On Tue, Dec 18, 2012 at 4:12 PM, Vedat Durmaz <dur...@zib.de> wrote:
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<
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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