AMBER Archive (2004)

Subject: Re: AMBER: Creating Parmtop files for NAMD

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Apr 14 2004 - 08:49:23 CDT

The amber parameters files have been converted to Charmm style topology
and parameters files
and can be used with with CNS (formerly xplor) or Charmm or NAMD to
create a psf/pdb pair.

This is an alternative to previous posting.

These files are available from either the Charmm website, a NAMD site or
the AMBER site (forgot which).
The most recent amber parameters may not yet be in Charmm format.

A protein structure file (psf) and pdb are the Charmm equivalent of an
AMBER parm/crd files created with tleap.

In short there are ways to mix and match AMBER/Charmm/NAMD/ (Gromos?)
that seem to be working these days.
But are not widely tested.

Thus my suggestion: (but if you don't have AMBER it doesn't apply )
Carefully check outputs from running AMBER and NAMD to make sure all agrees.
 From the number of atoms, types, bonds, angles, reported charge etc...
etc...

Dynamics at zero K can be directly compared between NAMD and amber (and
CNS and charmm for that matter) if SHAKE is not used and should give
you several timesteps with the same or nearly identical coordinates and
energies. If you read a velocity (restart file) you should also be able
to compare simulations at T !=0. This of course requires careful
attention to setting all possible options to corresponding values. The
NAMD manual provides some information on setting up an "amber" run in namd.

Note that both NAMD and AMBER apply shake before doing a timestep and
their implementation is different so that even the energies at the first
timestep will differ if shake is used.

Just my $0.0001
TOm

Edward Patrick Obrien wrote:

>Dear All,
> I am trying to use the AMBER force-field in NAMD. The problem I have is
>creating the parameter topology file, in AMBER format, for use in
>NAMD.
>
> I do not own the AMBER package and thus do not have access to LEAP
>which can create this file.
>
> My QUESTION is, is their any way to create the parm file of the system
>without having access to the entire AMBER suite of software? Is there a
>stand alone version of LEAP I could download?
>
>Any help would be appreciated.
>Regards,
>Ed
>
>PS- I've tried using the Cornell94 force-field in CHARMM format already.
>
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