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Thanks again Justin<BR>
<BR>
-----Original Message-----<BR>
<B>From</B>: Justin A. Lemkul <<A HREF="mailto:%22Justin%20A.%20Lemkul%22%20%3cjalemkul@vt.edu%3e">jalemkul@vt.edu</A>><BR>
<B>Reply-to</B>: "jalemkul@vt.edu" <jalemkul@vt.edu>, Discussion list for GROMACS users <gmx-users@gromacs.org><BR>
<B>To</B>: Gromacs Users' List <<A HREF="mailto:Gromacs%20Users'%20List%20%3cgmx-users@gromacs.org%3e">gmx-users@gromacs.org</A>><BR>
<B>Subject</B>: Re: [gmx-users] g_density CHARMM<BR>
<B>Date</B>: Tue, 11 Jan 2011 22:08:22 +0100<BR>
<BR>
<PRE>
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.
<A HREF="http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies">http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies</A>
<A HREF="http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml">http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml</A> (contact Prof. Karttunen for
the topology)
-Justin
> Ramon
>
> -----Original Message-----
> *From*: Justin A. Lemkul <<A HREF="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>
> <<A HREF="mailto:%22Justin%20A.%20Lemkul%22%20%3cjalemkul@vt.edu">mailto:%22Justin%20A.%20Lemkul%22%20%3cjalemkul@vt.edu</A>%3e>>
> *Reply-to*: "<A HREF="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>" <<A HREF="mailto:jalemkul@vt.edu">jalemkul@vt.edu</A>>, Discussion list for
> GROMACS users <<A HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>>
> *To*: Discussion list for GROMACS users <<A HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>
> <<A HREF="mailto:Discussion%20list%20for%20GROMACS%20users%20%3cgmx-users@gromacs.org">mailto:Discussion%20list%20for%20GROMACS%20users%20%3cgmx-users@gromacs.org</A>%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
> <A HREF="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A>
>
> ========================================
>
--
========================================
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
<A HREF="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A>
========================================
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