[gmx-users] g_density CHARMM

[Ramon Guixà]

Thanks again Justin

-----Original Message-----
From: Justin A. Lemkul <jalemkul at vt.edu>
Reply-to: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for
GROMACS users <gmx-users at gromacs.org>
To: Gromacs Users' List <gmx-users at gromacs.org>
Subject: Re: [gmx-users] g_density CHARMM
Date: Tue, 11 Jan 2011 22:08:22 +0100



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 <jalemkul at vt.edu 
> <mailto:%22Justin%20A.%20Lemkul%22%20%3cjalemkul at vt.edu%3e>>
> *Reply-to*: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for 
> GROMACS users <gmx-users at gromacs.org>
> *To*: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:Discussion%20list%20for%20GROMACS%20users%20%3cgmx-users at 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

========================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110112/1523447e/attachment.html>