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

From: LI An-Bang <>
Date: Mon, 17 Nov 2014 08:21:34 +0800


Thank you for the modified ambpdb program. It works well.

LI AnBang
 Physics Department, Central China Normal University, China


------------------ Original ------------------
From: "David A Case";<>;
Date: Fri, Nov 14, 2014 09:19 PM
To: "AMBER Mailing List"<>;

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

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.]

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Received on Sun Nov 16 2014 - 16:30:02 PST
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