From: Peter Freddolino (
Date: Wed Mar 27 2019 - 20:42:37 CDT

Hi James,
The amber-based extensions like sqm are not necessary for parameterizing
small molecules. The baseline building capabilities in molefacture,
combined with fftk, will suffice (as long as you have access to a machine
with Gaussian installed, but without that you're out of luck either way).
As I don't use windows, the best advice that I can offer is to try
installing the plain version of ambertools first, which is in general well
documented and supported by the amber community, and then one hopes that
you'd be able to make use of the patched ambertools tree distributed with
molefacture using the same approach.

On Wed, Mar 27, 2019 at 5:28 AM Stefan Boresch <>

> Hi James,
> [cc-ing this to the VMD list]
> I am afraid I can't help you, as (1) I use VMD for visualization only, and
> (2) use Linux as my main platform.
> My recent question about VMD/Windows on the list was concerned with
> getting a VMD version on students' laptops, which can download coordinates
> directly from the pdb.
> Ashar Malik's workaround for that
> (
> is a good fix for regular users, but I was afraid that it would not help
> novices too much.
> Hopefully some real Windows/VMD user can help you out!
> Stefan
> On Wed, Mar 27, 2019 at 02:13:04AM +0000, James T. Metz wrote:
> > Stefan,
> > Hello. I am attempting to get VMD 1.9.3 running properly on a
> WINDOWS 7 64-bit laptopcomputer. I am interested in being able to perform
> various calculations of small moleculesand proteins to obtain interaction
> energies and ultimately free energies. I am havingsome problems. I found
> your name on the VMD mailing list associated with WINDOWS,so I am assuming
> that you are using VMD on a WINDOWS computer.
> > Do you have possibly versions of sqm and antechamber from AMBER
> Tools that have
> > been properly compiled for VMD for WINDOWS 7 64-bit? I have obtained
> the latest version of AMBER Tools, I installed Cygwin, and I have tried
> several times to get everything compiled properly, but I am getting many
> error messages and I am not an expert at getting programs compiled
> properly! I am specifically interested inthese two programs at present, as
> they seem to be associated with the molefactureextension that seems to be
> necessary for parameterizing small molecules.
> > On the other hand, if you know of some way to obtain proper
> parameter files
> > for small molecules for VMD without using molefacture, I would be
> interested to learn your workflow.
> > I would appreciate hearing from you, or if you have code that you
> can share, I would be most grateful. Thank you.
> > Regards, Jim Metz
> > James T. Metz, Ph.D.
> > President, Metz Research LLC422 Cross RoadGurnee, IL 60031(847) 263 -
> 1514Please leave a message if you want a return
> >