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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Received on Wed Oct 29 2008 - 05:11:06 PDT
