AMBER Archive (2009)

Subject: [AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip)

From: Myunggi Yi (
Date: Wed Jun 24 2009 - 13:57:25 CDT

Dear Amber users,

If I use "strip" option to remove a part of the simulation system,
then PTRAJ writes out PDB files with "dumpq" option with wrong charges and
radii at the beginning of the PQR files.

If anyone else reproduces the same problem, then this is a bug.

One should not use "strip" option, to get right charges and radii (do some
post scripting to remove what you don't want).

I hope this can be fixed in the next version.

Best wishes,

Myunggi Yi ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306

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