Ramon Guixà wrote:
Justin,
Thanks for your response.
The membranes I've already run are made of POPC and cholesterol, so the
sphingomyelin membrane is my next simulation but I haven't managed to
find a proper forcefield for it. Would you know where to find this?
Not for CHARMM, no, but there are several available for different Gromos force
fields.
http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml (contact Prof. Karttunen for
the topology)
-Justin
Ramon
-----Original Message-----
*From*: Justin A. Lemkul <jalem...@vt.edu
<mailto:%22justin%20a.%20lemkul%22%20%3cjalem...@vt.edu%3e>>
*Reply-to*: "jalem...@vt.edu" <jalem...@vt.edu>, Discussion list for
GROMACS users <gmx-users@gromacs.org>
*To*: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:discussion%20list%20for%20gromacs%20users%20%3cgmx-us...@gromacs.org%3e>>
*Subject*: Re: [gmx-users] g_density CHARMM
*Date*: Tue, 11 Jan 2011 19:45:58 +0100
Ramon Guixà wrote:
Dear all,
I am just a newbie to Gromacs so sorry for being naive with my questions...
I would like to yield electron density profiles out of different
trajectories of membranes simulated with NAMD and last CHARMM forcefield
(all_36_lipid_cholesterol). I first tried to use pdb2gmx in order to
generate a GROMACS topology file that I could use for generating the
.tpr file needed for g_density. Well, I did not manage but is this the
proper way though?
Not likely. pdb2gmx is useful for creating topologies of macromolecules built
of repeating units (i.e. proteins and polymers). For lipid bilayers, it is far
more common to construct the topology as a set of #include statements, i.e.:
#include (forcefield)
#include "first_lipid_type.itp"
#include "next_lipid_type.itp"
etc.
Also, so far all my trajectories are .dcd files; does the g_density
function needs a .pdb file per frame? Otherwise, is it possible to
directly convert .dcd files into the gromacs .xtc ones?
Newer versions of Gromacs (>4.5) can read any file format that VMD can read, so
conversion is not necessary, provided you have the VMD libraries installed.
On another note, would anyone know where could I get proper topology and
parameter files of sphingomyelin?
If you already ran the simulations, do you not already have this? With the
information in Chapter 5 of the manual, you should be able to convert your
topologies from whatever format you have it in into the one required by Gromacs.
-Justin
Many thanks in advance!
Ramon
--
========================================
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
========================================
--
========================================
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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