AMBER Archive (2008)

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

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Tue Oct 28 2008 - 11:46:08 CDT

Question:

When we run antechamber to create NEWPDB.PDB and prepin files and assign
AMBER atom types it looks like the NEWPDB.PDB file has an incorrect format:

ATOM 18 H141AB1 1 -3.716 15.524 32.652 0.041810
ATOM 19 H142AB1 1 -5.014 15.668 31.441 0.044700
ATOM 20 H143AB1 1 -5.014 16.722 32.876 0.034220

Really our atom names here are "1H14" "2H14" "3H14" in the original PDB
file:

HETATM 61 1H14 AB1 X 1 -3.716 15.524 32.652 0.00
H 0
HETATM 62 2H14 AB1 X 1 -5.014 15.668 31.441 0.00
H 0
HETATM 63 3H14 AB1 X 1 -5.014 16.722 32.876 0.00
H 0

But something in antechamber is moving those prefix numbers into the
alternate location field of NEWPDB.PDB

Is this a known problem?

Thanks,

Bob Hanson 

-- 
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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