Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive

From: David A Case <>
Date: Fri, 14 Nov 2014 08:19:36 -0500

On Wed, Nov 12, 2014, LI An-Bang wrote:
> I used ambpdb to generate pdb and pqr files from .prmtop (there is chain
> ID information) and .inpcrd file, and find that options "-ext" and
> "-pqr" of ambpdb are exlusive.

Try using the attached ambpdb.F90 file in place of the on that is in
$AMBERHOME/AmberTools/src/etc. (Be sure to keep a copy of the original.)
Re-compile and give it a try...not tested, but it looks like it should
do what you want.

[Aside to Dan: (1) does cpp-ambpdb handle this combination? (2) add_pdb.F90
should be extended to include occupancy and B-factors from the original PDB
files...we have some upcoming uses for these.]


AMBER mailing list

Received on Fri Nov 14 2014 - 05:30:02 PST
Custom Search