AMBER Archive (2008)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Oct 28 2008 - 17:09:38 CDT

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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