Re: [AMBER] NPT at high pressure

From: Jason Swails <>
Date: Wed, 22 Aug 2012 10:19:46 -0400

On Wed, Aug 22, 2012 at 9:33 AM, Francesco Pietra <>wrote:

> Hi;
> I am using parm7 within NAMD. Is anything new with parm7 about
> carrying out equilibration of a protein in a water box? I mean, water
> model, flags? While range of temperatures have been explored, it seems
> that ff have been devised for 1 bar. Nonetheless, these are
> physiological conditions that would kill a deep water organism.

I'm confused... Is NAMD not running (and complaining about a badly
formatted topology file?). If it's 'running', then this is a question
about parameters and force fields, not so much the topology file...

If NAMD crashes, this is because NAMD does not adhere to the extensible
Amber prmtop format specification. I haven't tested the latest version of
NAMD, but NAMD 2.8 will not run with AmberTools12-generated topology file
because a couple extra flags were added to the prmtop, but they can be
deleted without much effort. The flags that are safe to delete (for use
and IPOL.

ParmEd can do this within its scripting environment, so a script that looks
like this:

outparm new_prmtop.parm7

You will need to use the "-e" flag to allow python commands in ParmEd to
use the above commands, though (note, ! is needed to activate the python
interpreter for that command).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Aug 22 2012 - 07:30:02 PDT
Custom Search