AMBER Archive (2004)

Subject: AMBER: Possible amber8 antechamber PDB parsing bug

From: Junmei Wang (JWang_at_encysive.com)
Date: Thu May 06 2004 - 12:09:30 CDT

Hi, Mark
Thank you for pointing out this. This problem only happens to the file of
NEWPDB.PDB generated by prepgen. The format of pdb files generated by
antechamber using the flag "-o pdb" is correct. I have made revision on
prepgen.c and will post another bugfix.

Best

Junmei

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

Dear amber users,

I have noticed a possible bug with amber8's antechamber. It manifests
itself in antechamber's PDB output when charge fitting using g03 output.
The gaussian output file (2.3 Meg) used in this example can be found at
http://dumb.ch.ic.ac.uk/~mjw99/share/mcg_b3lyp_6-31G*_opt.log

The command line used is:

$AMBERHOME/exe/antechamber -i mcg_b3lyp_6-31G\*_opt.log -fi gout -o
mcg.prep -c resp -fo prepi -nc 1

Upon examining the PDB output (NEWPDB.PDB):

With amber7:
-----------------

ATOM 1 C8 MOL 1 -2.429 0.672 -0.560 -0.11095
ATOM 2 H6 MOL 1 -2.362 1.640 -1.044 0.12412
ATOM 3 C9 MOL 1 -3.632 0.008 -0.576 -0.14637

With amber8:
-----------------

ATOM 1 C8 MOL 1 -2.429 0.672 -0.560 -0.11095
ATOM 2 H6 MOL 1 -2.362 1.640 -1.044 0.12412
ATOM 3 C9 MOL 1 -3.632 0.008 -0.576 -0.14637

The problems is with spacing (this may be lost here due to email
formatting), the 5 column is moved right by one space (26 --> 27) . This
causes viewers like VMD to fail. According to the PDB file format (
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html ):

23 - 26 Integer resSeq Residue sequence number.

27 AChar iCode Code for insertion of
residues.

This movement is significant since it is at a column boundary; resSeq is
being expressed as iCode. This has also been attempted amber8 with
patches 1-8 applied, with the same result.
Can anyone confirm the above problem?

regards,

Mark Williamson

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