ok but after I generated two .gro files using genconf (or editconf I
guess)
containing two identical proteins in different positions/orientations
how can I concatenate these two files in order to supply a unique .gro
file to grompp?
thanks Cristiano
Il giorno 10/mar/10, alle ore 16:27, Mark Abraham ha scritto:
----- Original Message -----
From: Cristiano De Michele <[email protected]>
Date: Thursday, March 11, 2010 2:25
Subject: [gmx-users] simulating several proteins
To: [email protected]
Dear all,
is it possible to simulate more than one protein with GROMACS?
I would like to simulate two lysozyme proteins not solvated and
I tried changing number of proteins in topology file (attached) and
then I used this modified .top file to generate a .gro configuration
with genbox, but I always end up getting just one protein
in the simulation box...
genbox doesn't take input from the .top file to guide its output.
Use genconf on your original structure file to multiply it. Then
edit your .top by hand to match.
Mark
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––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
Cristiano De Michele, Ph.D.
Department of Physics Tel. : +390649913524
University of Rome "La Sapienza" Fax : +39064463158
Piazzale Aldo Moro, 2
I-00185 Roma - Italy
homepage: http://pacci.phys.uniroma1.it/
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