VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Wed Sep 16 2009 - 15:37:17 CDT

Please note that NAMD supports amber parmtop files
so this might be a place to dig/look for support.
How's it handled in NAMD? does this help out hte VMD folks?
]
Tom

On Wednesday 16 September 2009, Axel Kohlmeyer wrote:
> 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.
>
> cheers,
> axel.
>
> > Best wishes, mike crowley
> >
> >
> > --------------------------
> > Sent using BlackBerry
> >
> >
> >
> > _________________________________________________________________
> >_____ 

-- 
**********************
Thomas C. Bishop     *
Office: 504-862-3370 *
Fax:    504-862-8392 *
**********************