[gmx-users] simulating several proteins

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 10 18:35:02 CET 2010

Cristiano De Michele wrote:
> 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?

If you run genconf correctly, then it should give you a proper .gro file, i.e.:

genconf -f oneprotein.gro -o twoprotein.gro -nbox 2 1 1

The above command will give two replicates of your protein aligned along the x axis.

If you have two unique orientations that you want to align, you can simply use 
editconf to assign their position within a box (with -center and -box 
simultaneously), and simply use the Unix 'cat' command to concatenate them. 
Then you have to update the second line of the .gro file to reflect the proper 
number of atoms and remove the superfluous headers and box vectors in the middle 
of the file.


> thanks Cristiano
> Il giorno 10/mar/10, alle ore 16:27, Mark Abraham ha scritto:
>> ----- Original Message -----
>> From: Cristiano De Michele <cristiano.demichele at roma1.infn.it>
>> Date: Thursday, March 11, 2010 2:25
>> Subject: [gmx-users] simulating several proteins
>> To: gmx-users at gromacs.org
>>> 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/
> ------
> "Shoot for the moon. Even if you miss, you'll land among the stars."


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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