Re: [AMBER] add_pdb

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 26 Apr 2012 08:56:20 -0400

Ptraj will only recognize the extra sections if you add the code yourself.

A workaround is to generate a restart file from your desired snapshot and use ambpdb to dump a PDB file with the correct numbering.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 26, 2012, at 4:39 AM, colvin <colvin4367.gmail.com> wrote:
> Hi,
> 
> Thank you for the reply. I can now use ambpdb with the vmd compatible
> chamber prmtop.
> 
> Is there a way for ptraj to recognise the extra section in the prmtop
> file? if i need to generate snapshot from trajectory and ptraj cannot
> read in the extra section, all the snapshot generated will have the
> residue numbering start from 1.
> 
> Pls advise.
> 
> Thanks and regards.
> Colvin
> 
> 
> 
> On Thu, Apr 26, 2012 at 10:21 AM, case <case.biomaps.rutgers.edu> wrote:
>> On Thu, Apr 26, 2012, colvin wrote:
>>> 
>>> 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?
>> 
>> I'm guessing that the chamber prmtop file has a CTITLE rather than a TITLE
>> command(?).  If so, It's certainly worth modifying ambpdb.F90 to look
>> for CTITLE rather than TITLE, and recompiling.  Ambpdb only uses a small
>> fraction of the information in the prmtop file, so may well be happy with such
>> a change.
>> 
>> ....dac
>> 
>> 
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Received on Thu Apr 26 2012 - 06:00:03 PDT
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