VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 16 2009 - 16:08:07 CDT

Tom,
  NAMD doesn't read any of the optional/extensible fields in
the AMBER prmtop files, it ignores anything it doesn't need for
simulation.

Cheers,
  John

On Wed, Sep 16, 2009 at 03:37:17PM -0500, Thomas C. Bishop wrote:
> 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 *
> ********************** 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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