Yan Gao wrote:
Thank you Vandana and Justin, the cat command solve the problem.
Regarding the removement of the unnecessary lines in the middle, is
there a command that can do it automatically? or one has to make code by
self? Thanks.
That's a trivial exercise for a simple text editor.
-Justin
Yan
On Tue, May 25, 2010 at 3:25 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
VANDANA KUMARI wrote:
Hi Yan,
You can do it by converting your both gro file into pdb files
and concatenating both pdb files into one file . and you can
convert pdb into gro using editconf
steps are as follows:
1. editconf -f 1.gro -o 1.pdb
2. editconf -f 2.gro -o 2.pdb
3. cat 1.pdb 2.pdb > both.pdb
you need to delete unnecessary line i.e. CRYST1 or END from you
both.pdb file
4. editconf -f both.pdb -o both.gro
Conversion back and forth between .pdb and .gro is not required (but
it does work). The main point of creating a concatenated file is
that both molecules are placed correctly within the same box, so for
each:
editconf -f 1.gro -o 1_newbox.gro -center x y z -box x y z
(and the same for molecule 2)
Getting the molecule positions and box vectors right is the real trick.
Then concatenate, remove unnecessary box and header lines in the
middle of the file, correct the atom count and you're done.
-Justin
--
Vandana Kumari
------------------------------------------------------------------------
*From:* [email protected]
<mailto:[email protected]>
[[email protected]
<mailto:[email protected]>] on behalf of Yan Gao
[[email protected] <mailto:[email protected]>]
*Sent:* Tuesday, May 25, 2010 5:33 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] How to combine two gro files in one big file
Hi there,
I want to simulate two molecules which are identical, and one is
rotated/translated from another. I have the gro file for one
molecule.
I tried editconf, which helped manipulate the molecule. Then I
want to combine it with the original gro file, so that the two
identical molecules are placed in one file. I searched the
manual but could not find a proper command. Could anyone help?
Thanks.
--
Yan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: [email protected] <mailto:[email protected]>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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