Re: Using Amber FF in NAMD

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Mar 18 2009 - 18:38:31 CDT

On Wed, 2009-03-18 at 16:13 -0700, Joshua Adelman wrote:
> I am attempting to use one of the amber force field parameter sets in
> namd, and am getting the error:
>
> Info: Using AMBER format force field!
> Info: AMBER PARM FILE ../parm98.dat
> Info: COORDINATE PDB ../xxx_ionized.pdb
> Info: Exclusions will be read from PARM file!
> Info: SCNB (VDW SCALING) 2
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Reading parm file (../parm98.dat) ...
> FATAL ERROR: Failed to read AMBER parm file!
>
> I am using parm98.dat found in the distribution available at:
> http://ambermd.org/dbase.html
>
> The namd UG says that namd should be able to read parm files in
> either the Amber 6 or 7 format, although it was unclear to me if
> there has been another change in the format between Amber 7 and the
> most recent distribution. If anyone has a suggestion or could point
> me to versions of the force fields (parm98 or parm94 and ff98sb), I
> would appreciate it.
>
> Also, the UG says that, " If amber is set to on, then parmfile must
> be defined, and structure and parameters should not be defined." If
> you are using a pdb file for the coordinates, how does namd deal with
> not having a psf or similar topology file. as is required in a
> standard run with the charmm force field?

josh,

amber's parmtop files have the parameter _and_ topology
information combined in one file.

cheers,
   axel.

>
> Josh
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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