AMBER Archive (2009)

Subject: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Mar 02 2009 - 08:56:54 CST

On Mon, Mar 02, 2009, ?????? wrote:
>
> What should I do if I have my own pdb file and sustive is just part of it?

You would have to use loadmol2 to load the (modified charge) description
of the sustiva. What follows next depends on what is in the rest of the
pdb file. If the rest of the pdb file is a protein, then LEaP will
recognize it. If the rest of the pdb file is some non-protein part, you
would have to create mol2 files (or the equivalent) for these remaining
parts, and load them before you load the pdb file.

Be sure to put TER cards in the pdb file around each separate molecule
(e.g. before and after the sustiva part).

...good luck...dac

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