Re: [AMBER] Constant values in prmtop

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 9 Jan 2015 07:03:25 -0500

On Fri, Jan 9, 2015 at 4:45 AM, Mohd Farid Ismail <
mohd.farid.ismail.yandex.com> wrote:

>
> Hi, in the prmtop file, under the FLAG BOND_FORCE_CONST and
> BOND_EQUIL_VALUE, how do I determine which value is connected to which
> bond?
>

‚ÄčThese sections are just "tables" of parameters. The BONDS_INC_HYDROGEN
and BONDS_WITHOUT_HYDROGEN sections contain pointers into these arrays for
each bond. So each number does not necessarily correspond to a single (or
any) bond -- they in fact usually correspond to many different bonds (that
all have the same parameters).

The prmtop file is not really human-readable in this way. I would suggest
using a tool like ParmEd or cpptraj to inspect the prmtop file.

You can also find documentation about the file format at
http://ambermd.org/formats.html if what you're trying to do is fully
understand the prmtop.

HTH,
Jason
‚Äč
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 09 2015 - 04:30:05 PST
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