VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Feb 15 2012 - 10:24:11 CST

Hi Stefan,

By "the PSF builder" do you mean VMD's autopsf plugin or the psfgen module
that actually parses the topology files? (I can assure you psfgen knows
nothing about phosphates beyond what is in the topology files.)

If you can tell me precisely what you are doing (I'm not a biochemist) and
what the unwanted behavior is I can tell you why it is happening.

-Jim

On Wed, 15 Feb 2012, John Stone wrote:

>
> Can you reply to this Prof. from NC state?
>
> ----- Forwarded message from Stefan Franzen <Stefan_Franzen_at_ncsu.edu> -----
>
> Date: Mon, 13 Feb 2012 10:31:12 -0500
> Subject: vmd-l: Patch for deoxy and dideoxy nucleotides
> From: Stefan Franzen <Stefan_Franzen_at_ncsu.edu>
> To: vmd-l <vmd-l_at_ks.uiuc.edu>
>
> We are trying to create a patch for nucleotides that consists of both
> 2'-deoxy and 2'-O methyl ribonucleotides. The default deletes 2'-O methyl
> so it appears necessary to develop a patch. However, there must be an
> internal patch since the PSF builder automatically puts a second phosphate
> into the patch that we added. We need to understand how to design a patch
> that is consistent with the internal workings of the PSF builder, but have
> no way to do this without knowing the precise way that the PSF builder
> works.
>
> --
> Stefan Franzen
> Professor of Chemistry
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-515-8915
>
> ----- End forwarded message -----
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>