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:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Yan Gao [y1...@ucsd.edu]
*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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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