Re: [AMBER] format error from

From: Mark Williamson <>
Date: Mon, 13 Jun 2011 10:58:25 +0100

Jason Swails wrote:
> It appears as though the topology file class doesn't work with chamber topology files... I've never seen one of those topology files, and I didn't know anything was that fundamentally different with them.


The modifications are made to accommodate the CHARMM specific terms in
the AMBER prmtop file and these are outlined on p 37 of the ambertools
1.5 manual. The chamber prmtop file adheres to the amber prmtop 7 file
format (i.e. %FLAG FOO, %FORMAT(FOOFORMAT), FOO(i) ). It has some extra
terms and some existing terms have had their formats altered, the
reasons behind these are also covered in the manual.

The ntxsec() routine in the Fortran codes (SANDER and PMEMD), readily
and correctly parses these extra terms, however, many other codes
(mainly C) ignore the FORMAT flag associated with a FLAG, and instead,
rely on a hardcoded associated format string for that FLAG.



AMBER mailing list
Received on Mon Jun 13 2011 - 03:00:02 PDT
Custom Search