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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 09 2011 - 07:30:05 PST
