Re: [AMBER] add_pdb

From: colvin <>
Date: Thu, 26 Apr 2012 16:39:46 +0800


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.

On Thu, Apr 26, 2012 at 10:21 AM, case <> 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Apr 26 2012 - 02:00:04 PDT
Custom Search