Re: [AMBER] Can we load rst files in leap?

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 12 Jan 2011 11:22:43 -0800

> 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.

You need to use the pdb, loadpdb, solvate, and saveamberparm.
There is no such thing as an 'atom type' column in pdb that
leap requires. If you have the same setup as when you generated
the vacuum saveamberparm, the pdb should load ok. If you send
whatever error/warning messages you are seeing, we can diagnose


AMBER mailing list
Received on Wed Jan 12 2011 - 11:30:04 PST
Custom Search