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 - 04:30:03 PST
