VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 16 2009 - 13:46:26 CDT

Hi Michael,
  I'm working on adding support for arbitrary extensible
per-atom, per-residue, and per-molecule data fields into the
VMD molfile plugin interface, followed by support in the VMD
atom selection language, graphical user interfaces, and so on.
I don't know how hard it will be for me to support these features
for the AMBER prmtop reader plugin, but I would expect that
these could be supported. The ability to order the sections in
any order shouldn't be much of a problem, but the existing plugin
wasn't designed to allow this, as it is a derivative from
much older C-based AMBER prmtop readers that had a fixed ordering
assumption.

The issue you mention with the variation in format specifier for the
title string should be minor and trivial to fix. I would be happy
to help work on addressing these issues with the time that I have
available. If you can provide sets of test files on the biofs, that
would be an excellent way to get the ball rolling.

Going forward, it would be great if someone from the AMBER team
was willing to help us maintain the various AMBER reader plugins for VMD,
since someone with a strong AMBER background would be more familiar with the
minutiae of these files than I would be. I know that nobody has free
time coming out of their ears, but it would definitely benefit the AMBER
user community to make these plugins a bit more bulletproof and significantly
more flexible. I often find it difficult to procure test files when
I'm singlehandedly maintaining these plugins, so just having one AMBER expert
that's committed to helping out with developing, testing, planning
this stuff would be great.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 16, 2009 at 11:21:42AM -0600, Crowley, Michael wrote:
> 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?
>
> 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.
>
> If you can help at this time to get us going with the new prmtop, we can
> send an example prmtop/inpcrd. Thanks.
> Best wishes, mike crowley
>
> --------------------------
> Sent using BlackBerry
>
> --------------------------------------------------------------------------
>
> From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu>
> To: Luca Gelisio <luca.gelisio_at_gmail.com>; VMD Mailing List
> <vmd-l_at_ks.uiuc.edu>
> Sent: Wed Sep 16 07:01:57 2009
> Subject: Re: vmd-l: segid WT100 is longer than 4 characters allowed by psf
> format
> Hi Luca,
> Surely. By changing from segid prefix from WT toA W, you can increase the
> character space.A
> best,
> Ramya
>
> On Wed, Sep 16, 2009 at 3:34 AM, Luca Gelisio <luca.gelisio_at_gmail.com>
> wrote:
>
> Hi to all,
>
> when generating a large solvation box (extension -> modeling -> add
> solvation box), keeping options "waterbox only" and "rotate to
> minimize volume", the error:
> "segid WT100 is longer than 4 characters allowed by psf format"
> appear on the terminal. I am running VMD on a i7 machine with a GTX285
> plus a GTX295, 6 Gb RAM, on Linux Ubuntu (2.6.28-15).
> The largest waterbox I have generated is 18x18x18 nm. Is it possible
> to generate a larger one?
>
> Thanks,
> luca 

-- 
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
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078