On Mon, Jun 13, 2011, Mark Williamson wrote:
>
> 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.
Two quick points:
1. I've added a check for a CTITLE in NAB's routine that reads prmtop files.
Since the NAB energy functions don't have the CHARMM extensions, this just
exits with an error message.
2. It's correct that NAB doesn't process the %FORMAT files, but rather assumes
that all entries are white-space delimited. Informally, at least, it would be
good if routines writing prmtop files also did this. More rigorously, we
should modify the NAB routines. In the old days, NAB was pure "C" code, and
this was harder to do. Now that we require both C and fortran compilers for
NAB, it would be much simpler to implement the logic that is in sander.
....dac
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Received on Mon Jun 13 2011 - 06:00:03 PDT
