AMBER Archive (2008)

Subject: Re: AMBER: NAB documentation

From: Ramu Anandakrishnan (ramu_at_vt.edu)
Date: Fri Jun 06 2008 - 23:08:51 CDT

Thanks Dave. Anything Tom has could be helpful.

In the meantime I do have a couple of questions:

1. We're getting a segmentation fault when trying to run NAB on a molecule
with multiple chains (strands). Do you know if NAB has been tested with
multiple strands?

2. There is a c data structure with "MOLECULE_T.m_natoms" and a NAB data
strucutre with "molecule.natoms", but the two don't seem to have the same
value, even though "MOLECULE_T" is assigned to "molecule" in getpdb_prm.nab.
Do you know how/where molecule.natoms is updated?

Regards
Ramu

----- Original Message -----
From: "David Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Friday, June 06, 2008 12:24 PM
Subject: AMBER: NAB documentation

> On Wed, Jun 04, 2008, ramu_at_vt.edu wrote:
>
>> I would like to modify the NAB code to test a new MD method. Is there any
>> documentation describing the code (data structures, program flow, etc.),
>> besides the user's guide?
>
> cc-ing to Tom Macke. At one point, there was some internal documentation,
> but
> I suspect it's so old now as to not be of much use.
>
> Of course, the real hope is that the md() routine (in sff.c) is simple
> enough
> that one can understand it without the need for additional information. I
> think it is pretty straightforward [one main "for" loop over MD steps...]
>
> ...good luck...dac
>
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