Re: [AMBER] add_pdb

From: David A Case <>
Date: Wed, 25 Apr 2012 08:26:51 -0400

On Wed, Apr 25, 2012, colvin wrote:
> From the previous entry in amber archive, i came to know about this
> program, add_pdb that add residue and atom information to the prmtop
> file. I tried it and it did added in %FLAG RESIDUE_number in the new
> prmtop file. I then used this new prmtop file to generate a pdb file,
> (by traj in inpcrd file and traj out pdb) but the output pdb file does
> not come with the original residue numbering, and it is numbered from
> 1.

Ptraj doesn't know anything about the extra sections in the prmtop file.
Use ambpdb with the "-ext" flag to convert a prtmop/inpcrd file pair
into a pdb file, making use of the extra information.


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Received on Wed Apr 25 2012 - 05:30:07 PDT
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