thank you very much for the useful hints!
Cristiano
Il giorno 10/mar/10, alle ore 18:35, Justin A. Lemkul ha scritto:
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.
-Justin
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/
------
"Shoot for the moon. Even if you miss, you'll land among the stars."
--
========================================
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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––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
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."
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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