VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 12 2009 - 15:50:56 CDT

Hi,
  I think that a likely solution to this problem will arise when we finish
updating psfgen to allow support for a broader diversity of VMD plugins and
file formats. This would enable one to emit the resulting structure
in one of several other file formats that don't suffer from limited
length data fields. We are already working on this in support of some work
with very large simulations in my research group, but there's more to do
and so at present it is an experimental implementation. I will let people
know when the updated psfgen is available. In the mean time, you may find
it easier to workaround this problem by modifying your atom types etc to fit
within the limitations of the non-extended PSF format used by the currently
available version of psfgen.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 08, 2009 at 06:19:26PM -0300, Alexandre Suman de Araujo wrote:
> Hi All
>
> I'm using psfgen to generate the topology to beta-cyclodextrin using
> charmm carbohydrate parameters obtained from this site:
> http://mackerell.umaryland.edu/CHARMM_ff_params.html.
>
> When I load the generated psf in VMD the total charge of the model is
> about 60! The problem is that the names used in the parameters file are
> bigger than the associated field and the number at the end of atom type
> is read as the atom charge (the next field). For example, the CC3161
> atom type have 0.09 as charge in the parameter file but VMD read its
> charge as 1.0 (because de number 1 at the end), the CC3162 have a charge
> of 2.0 (because de number 2 at the end) associated to it instead of 0.34
> as defined in the parameter file.
>
> Did anyone also deal with this problem??? I think the solution is to
> change all names in the parameters files, but if someone have a smarter
> solution I appreciate to know it.
>
> Cheers
>
> --
> **************************************************************
> Alexandre Suman de Araujo *
> Faculdade de Ciências Farmacêuticas de Ribeirão Preto *
> Universidade de São Paulo *
> Dep. de Física e Química *
> Grupo de Física Biológica * e-mail: asaraujo_at_fcfrp.usp.br*
> Av. do Café, s/n° * e-mail: ale.suman_at_gmail.com *
> CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
> Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
> ************************************************************** 

-- 
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