RE: biotin parameters and topology

From: Brian R Novak (bnovak1_at_lsu.edu)
Date: Tue Apr 28 2009 - 15:43:15 CDT

Peter,

Thanks a lot. This will save me a lot of time.

Brian

-----Original Message-----
From: Peter Freddolino [mailto:petefred_at_ks.uiuc.edu]
Sent: Tue 4/28/2009 3:13 PM
To: Brian R Novak
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: biotin parameters and topology
 
Hi Brian,
I didn't, in point of fact, send the parameters (I don't have them), but
rather, passed the request along to someone who had worked on that
particular system. I will do so again.
Best,
Peter

Brian R Novak wrote:
> 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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