From: Axel Kohlmeyer (
Date: Wed Sep 16 2009 - 13:28:37 CDT

On Wed, 2009-09-16 at 11:21 -0600, Crowley, Michael wrote:

dear mike,

> Dear vmd folks, this msg is for developers. The so-called amber7
> prmtop format is designed for flexibility and allows for new data
> sections and different formats by specifying the field name and format
> for each field. It also allows the sections to be in any order. Will
> vmd be supporting this flexibility soon?

although i have no authority to speak on behalf of the VMD developers,
i would like to point out that the majority of the plugins in the
molfile library are _contributed_ software and merely "kept alive"
or fixed to accommodate changes that happen internally in VMD. so
the first line of attack would be to track down the original developer
or the current maintainer of the plugin source and discuss changes.

it has become the nature of our business that people work on something
they need until it does what they need, so that quite often plugins
are in a half-ready state until somebody else picks them up and
implements what is needed, and so on. at least this is how i understand
things work and how i got molfile plugins fixed that i needed fixed,
or support for new file formats added, i.e. by digging into the source
code and changing or implementing it myself.

> Our main concern is that we have added the ability to use current
> charmm ff to amber necessitating new ff sections and some different
> formats which all follow the prmtop standard. We are not able to read
> these prmtops into vmd. I do not know if it is just the title but that
> is where it fails now. Vmd appears to require the format to say 20a4
> when we are using a80. Seems harmless from the amber stndpopint but
> breaks vmd.

also improvements to the plugins to add support for recent additions to
the molfile API (support for reading/writing angles, dihedrals, and
impropers) have already been requested on this list...

> If you can help at this time to get us going with the new prmtop, we
> can send an example prmtop/inpcrd. Thanks.

example files, preferable with some variability, are always highly
welcome and i know that there is a repository of test files somewhere.

the best way to communicate files to 'the VMD developers' is via
depositing them into the VMD biocore project biofs.


> Best wishes, mike crowley
> --------------------------
> Sent using BlackBerry
> ______________________________________________________________________

Dr. Axel Kohlmeyer 
Research Associate Professor
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.