Re: [AMBER] Constant values in prmtop

From: Jason Swails <>
Date: Fri, 9 Jan 2015 07:03:25 -0500

On Fri, Jan 9, 2015 at 4:45 AM, Mohd Farid Ismail <> 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 if what you're trying to do is fully
understand the prmtop.

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