biotin parameters and topology

From: Brian R Novak (bnovak1_at_lsu.edu)
Date: Tue Apr 28 2009 - 12:37:53 CDT

Dear NAMD users:

I need the CHARMM parameters and topology for biotin to simulate biotin carboxylase with bound biotin.

This paper says they can be found at ftp://ftp.ks.uiuc.edu/, but this does not seem to exist anymore.

Molecular dynamics study of unbinding of the avidin-biotin complex
Author(s): Izrailev S, Stepaniants S, Balsera M, Oono Y, Schulten K
Source: BIOPHYSICAL JOURNAL Volume: 72 Issue: 4 Pages: 1568-1581 Published: APR 1997

Does anyone know if I can download these anywhere? Perhaps they should be put on NamdWiki.

Peter,

I found a conversation where you sent someone these files (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7801.html). There was an attached topology file. Is this the topology used in the above paper, and are all of the parameters in the CHARMM topology files or do I need a parameter file as well?

Thanks for any help,
Brian

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