Re: pdbalias for PO4 residue

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sat Jul 11 2009 - 19:37:53 CDT

You will need to create a topology and parameters for PO4 if they are not
otherwise available.

See here:
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/

and for example files here:
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-tutorial-files.tar.gz

Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Sat, Jul 11, 2009 at 1:09 AM, gurunath katagi <gurukatagi_at_gmail.com>wrote:
> Hello everyone,
>
> the pdb file for which  I want to create psf file contains PO4 residue ..
> when i run the script to create the psf file..it gives an error
> Unknown residue PO4..
>
> i checked in the topology file for PO4 residue... there is only entry for
> atoms of PO4...how do i include them  in the psf file...
> or is there any pdblias for PO4 resdue...
>
> the part of the pdb file is pasted here:
> HETATM 4432  P   PO4 B 147       5.931 -21.573   3.319  1.00
> 32.97           P
>
> thank you
> Gurunath
> --
> Gurunath M Katagi
> M.Sc (engg) Research student
> Supercomputer Education and Research Centre
> Indian Institute Of Science
> Bangalore
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:12 CST