AMBER Archive (2008)

Subject: Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Tue Oct 28 2008 - 17:42:19 CDT

Great, thanks. Any easy way to have an AMBER tool add the H atoms for us?

Bob

On Tue, Oct 28, 2008 at 5:09 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Tue, Oct 28, 2008, Robert Hanson wrote:
> >
> > Problem: We have a ligand that is part of a PDB file from RCSB. No H
> atoms
> > and no AMBER atom types.
> >
> > a) We use another program to add H atoms (that's when these H atoms get
> > named in this way), creating xxxxH.PDB.
> > c) We feed xxxxH.PDB into antechamber to assign GAFF atom types.
> > d) We use NEWPDB.PDB for the correctly ordered set of atom coordinates
> > e) We use prepin for the correct atom types.
>
> Try using the mol2 output format -- this will get atom types, and will
> preserve the atom order.
>
> > f) We merge these by hand by first saving them in leap using saveoff and
> > then cutting and pasting.
> > g) We load the merged OFF file to create our desired PDB file.
>
> You should be able to then load the mol2 file (using loadmol2 rather than
> loadoff) and create the desired pdb file.
>
> Thanks for your comments and problem reports. If the mol2 scheme doesn't
> work
> they way you need, please let us know -- I'd like to get rid of the prep
> and
> off formats, pushing everything to mol2, since that format is understood by
> lots of other programs. But if there are things mol2 can't do, we need to
> find that out, (and fix if possible).
>
> ...thx...dave
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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