Hi,
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
workaround?
Thanks and regards,
Colvin
On Wed, Apr 25, 2012 at 8:26 PM, David A Case <case.biomaps.rutgers.edu> 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
>
>
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Received on Wed Apr 25 2012 - 17:30:09 PDT
