VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 17 2009 - 12:50:48 CDT

Michael,
  I haven't heard anything back since my reply yesterday, but if you can
provide example files that you're having trouble loading, that would
be very helpful.

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