From: youbin tu (youbint_at_gmail.com)
Date: Fri Aug 11 2006 - 13:38:22 CDT
Thanks Leo. I found it in stream file. Actually I want the parameter for
cysteine linked heme, I used to think PSUL should be. But it seems that it
is only methylthiolated heme there. It can not handle my problem at all. I
need suggestion on how to create/modify parameter or even topology files to
fit in the cysteine linked heme. Also I just wonder why anyone in NAMD group
just created the parameters for cysteine linked heme since histidine linked
heme parameters have already existed long long time before?
I am pretty sure there are a lot of groups working on cysteine linked
heme protein, did they all have to create the parameters themselves?
Youbin
On 8/10/06, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:
>
> On Thu, Aug 10, 2006 at 12:01:50PM -0400, youbin tu wrote:
> > I was trying to simulate P450, but the heme cysteine link still
> troubled
> > me a lot. I found out that there seems to be PSUL(heme to sulfate link)
> in
> > the parameter file, but I could not find the corresponding patch in
> topology
> > file. Can you tell me where can I find the PSUL patch?
>
> If you grep the files downloaded from Mackerell's web page, you'll see
> that there's a PSUL patch in the file stream/toppar_all22_prot_heme.str.
> I don't know if this is what you're looking for.
>
> Best,
> Leo
>
> --
> Leonardo Trabuco, Ph.D. candidate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
>
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