AMBER Archive (2008)

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

From: Robert Hanson (
Date: Tue Oct 28 2008 - 13:21:59 CDT

Right, that's the issue -- it appears that any four-character PDB atom name
is output incorrectly to NEWPDB.PDB.

I'll try to stick to 3-letter PDB atom names.

Why my interest in NEWPDB.PDB? Maybe there's a different way of solving this
problem. I'm sure there's a better way to do the following:

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.
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.

A better way that avoids using NEWPDB.PDB must exist. Yes?


On Tue, Oct 28, 2008 at 12:57 PM, David A. Case <>wrote:

> On Tue, Oct 28, 2008, David A. Case wrote:
> > > But something in antechamber is moving those prefix numbers into the
> > > alternate location field of NEWPDB.PDB
> Oops...I guess my previous post missed the problem that the atom names in
> the
> NEWPDB.PDB file might be in the wrong columns. This should be fixed,
> (although
> I must say that I have never made use of the NEWPDB.PDB file, and am not
> even
> sure why it is written out.)
> Sorry for the confusion...dac
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
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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