[AMBER-Developers] [bap.legrand.gmail.com: [AMBER] Can we load rst files in leap?]

From: David A. Case <case.biomaps.rutgers.edu>
Date: Wed, 12 Jan 2011 15:19:31 -0500

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.


----- 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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Received on Wed Jan 12 2011 - 12:30:02 PST
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