I added a -mol2 flag to do that. The mol2 file produced conforms to leap's
interpretation of the mol2 format, I believe (at least it mirrors the mol2
printed by savemol2). Leap seems to read the ones I tested it on. I also
included one of my little tools to extract the parameters from a prmtop and
dump it into an frcmod file so it should be pretty painless to back out
starting files if they've been misplaced (or you were just given a prmtop by
somebody).
All the best,
Jason
On Wed, Jan 12, 2011 at 3:19 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> It would (I think) be doable to augment ambpdb to have a -mol2 flag that
> would output a mol2 file rather than a pdb file. Just seeing if anyone
> wants
> to volunteer....
>
> There could also be a "mol2" flag to the trajout command in ptraj or
> cpptraj.
> That is a little clunkier, since people might not think of ptraj as having
> that capability, but would also skin the cat.
>
> ...dac
>
>
> ----- Forwarded message from Baptiste Legrand <bap.legrand.gmail.com>
> -----
>
> Date: Wed, 12 Jan 2011 19:36:04 +0100
> From: Baptiste Legrand <bap.legrand.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Can we load rst files in leap?
>
> I want to use structures from a previous MD run in vacuum to launch a
> run in a solvent box. Is it possible to load directly my rst and prmtop
> files in leap to create "solvated" starting files?
> For the moment, I have convert the rst files in pdb using ambpdb
> nevertheless the generated pdb don't have the 'atom type' column and
> cannot be loaded in leap.
>
> ----- End forwarded message -----
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 13 2011 - 13:30:03 PST
