Re: [AMBER] add_pdb

From: colvin <>
Date: Thu, 26 Apr 2012 08:02:06 +0800


Thanks for the reply, but my prmtop file is actually generated from
chamber, i cannot use ambpdb to get pdb file because it gives me
error: ERROR: Flag "TITLE" not found in PARM file. Is there any other

Thanks and regards,

On Wed, Apr 25, 2012 at 8:26 PM, David A Case <> wrote:
> 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.
> ....dac
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Apr 25 2012 - 17:30:09 PDT
Custom Search