AMBER Archive (2002)

Subject: ambpdb in AMBER7

From: Matthew Lee (mrlee_at_cgl.ucsf.edu)
Date: Wed May 22 2002 - 15:42:34 CDT

I am interested in getting Brookhaven PDB format from my restart file.
According to the AMBER7 documentation, this should be possible with
the -aatm flag of ambpdb. However, it seems that the -aatm flag wipes
out atom types altogether. Has anyone else seen this problem:

------------------------------------------------
milo 694% ambpdb -p xyz.vac94.top < xyz.crd | head 5
| New format PARM file being parsed.
| Version = 1.000 Date = 05/16/02 Time = 11:05:44
REMARK
ATOM 1 N THR 1 23.412 -6.004 13.583
ATOM 2 H1 THR 1 22.703 -6.717 13.491
ATOM 3 H2 THR 1 23.402 -5.656 14.531
ATOM 4 H3 THR 1 24.315 -6.293 13.236
ATOM 5 CA THR 1 23.030 -4.886 12.764
milo 695% ambpdb -aatm -p xyz.vac94.top < xyz.crd | head -5
| New format PARM file being parsed.
| Version = 1.000 Date = 05/16/02 Time = 11:05:44
REMARK
ATOM 1 THR 1 23.412 -6.004 13.583
ATOM 2 THR 1 22.703 -6.717 13.491
ATOM 3 THR 1 23.402 -5.656 14.531
ATOM 4 THR 1 24.315 -6.293 13.236
ATOM 5 THR 1 23.030 -4.886 12.764
------------------------------------------------

--Matt Lee

*******************************************************************
Matthew Randolph Lee, Ph.D.

Computational Scientist phone: (858)410-6534
Lion Bioscience Inc. fax: (858)410-6665
9880 Campus Point Drive e-mail: matthew.lee_at_lionbioscience.com
San Diego, CA 92121
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