Re: [AMBER] Membrane building

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Sat, 19 Nov 2011 14:22:38 +0100

We describe extended simulations with the gaff force field for popc in a paper in the august issue of plos computational biology

However, the amber software is not suitable for such simulations as it does not provide alternative pressure control schemes required for these simulations

Bottom line is if you want to use the gaff force fields, you need to use NAMD for the simulations

Leap is also pretty rudimentary for membrane simulations ...

Vlad

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Dr. Vlad Cojocaru
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madhumita das <madhumita.bioinfo.gmail.com> wrote:
Dear David,
Thanks for your kind reply I tried as u suggested but what is the
charge type i will choose to run antechamber in order to convert a psf
file to a frcmod file? Is there any other module in amber to convert charmm
parameters to amber parameters?
On Wed, Nov 9, 2011 at 8:43 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Nov 08, 2011, madhumita das wrote:
>
> >
> > I want to generate prmtop and inpcrd files for
> the
> > pdb file of lipid POPE ( obtained from VMD) by using xleap so that I
> > could be able to convert it in gromacs format? am I going in the right
> > path? How can I simulate a membrane protein in AMBER? Please guide this
> > beginner.
>
> You are tackling a difficult problem for a beginner, especially if your
> only
> goal is to use Amber as an intermediate format to go from VMD to gromacs.
> Compounding this is the fact that few amber developers (and, I suspect
> relatively few Amber users[?]) are using this code for membrane/protein
> simulations.
>
> But the broad outline is to use antechamber (as outlined in Tutorial B4) to
> create a library and frcmod file for a single POPE molecule. Then use LEaP
> to load the library, plus the lipid (bilayer?) coordinates you got from
> VMD,
> and save the prmtop and inpcrd files. Then (I guess) there may be some
> conversion script that will move these to gromacs (I have no experience
> with
> that part.)
>
> Have you asked this question of the gromacs support people? Seems to me
> that
> there must be easier ways to do what you describe....
>
> ....dac
>
>
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Received on Sat Nov 19 2011 - 05:30:02 PST