RE: convert .xyz file in .psf file for non-protein molecule

From: Radak, Brian K (
Date: Thu Sep 08 2016 - 12:39:04 CDT

This is a common enough problem that several groups are looking into (relatively) general solutions for it. Just to advertise the work of my colleagues, General Automated Atomic Model Parameterization (GAAMP), is one such method. To my knowledge this can be used compatibly with AMBER (GAFF) and CHARMM (CGenFF) force fields.

You can find the GAAMP server here:


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

From: [] on behalf of Axel Kohlmeyer []
Sent: Thursday, September 08, 2016 10:41 AM
To: NAMD list;
Subject: Re: namd-l: convert .xyz file in .psf file for non-protein molecule

On Thu, Sep 8, 2016 at 11:20 AM, <> wrote:
> Dear NAMD users,
> I am a new user of NAMD MD simulations. I work with this non-protein
> molecule in attachment. Its structure is alrealy optimized (in DFT), so I
> just want to convert this .XYZfile in .PSFfile to perform MD simulation on
> it.
> I search in the mailing list and in different tutorials how to do this but
> I don't find the solution.

that is because you have a lot of work ahead of you. having an
optimized geometry is about the least important piece of information
required for a simulation. a PSF file doesn't contain anything of it.
what you need instead are assignment of force field atom types,
(partial) charges, topology information like bonds, angles, dihedrals,
perhaps impropers. ...and since you are using a non-standard
molecule/residue, you may have to spend some time deriving and
determining force field parameters for it. for somebody that is new to
MD, that is a huge amount of work, and particularly assigning/deriving
force field parameters can be complex and may require a lot of testing
and additional computations.

> So I very appreciate any help to do this

your best chance to get something going, is probably to find a
collaborator that has the experience and knowledge in working with
custom molecules.


> Regards
> Benjamin Grenier
> Cinam CNRS, France

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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