Re: RE: about topology generation

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Dec 05 2006 - 01:34:08 CST

Hi Sting
Have a look at this article. i think there is amber parameter for
cyanocobalmine but i am not sure. there may be some charmm parameter also.
you can search google or may be ncbi.
*Journal of Molecular Structure*
<http://proxy.mul.missouri.edu:2159/science?_ob=PublicationURL&_cdi=5262&_pubType=J&_auth=y&_acct=C000049994&_version=1&_urlVersion=0&_userid=3419478&md5=a1ac35776aa0ee54e287c83bfbc2ddd8>
Volume 561, Issues
1-3<http://proxy.mul.missouri.edu:2159/science?_ob=PublicationURL&_tockey=%23TOC%235262%232001%23994389998%23240807%23FLA%23&_cdi=5262&_pubType=J&view=c&_auth=y&_acct=C000049994&_version=1&_urlVersion=0&_userid=3419478&md5=2d3fca36c3433599004b9669ff0c28d2>,
12 April 2001, Pages 71-91

Dhiraj

On 12/5/06, Sting <stg1979_at_emails.bjut.edu.cn> wrote:
>
> Dear JC Gumbart,
> I want to perform a SMD to pull the B12 through a channel. I try to
> generate a gromacs topology using the web server"
> davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/" and hope to convert it to
> charmm format, but it can't handle the metal Co.
> DO you have any suggestion?
> Thank you a lot!
>
> ====
>
> >For what purpose do you need this? I think there are some Amber and
> Gromacs
> >parameters out there, but no Charmm that I know of. It's certainly a
> very
> >difficult molecule and there may be no appropriate template in Charmm
> >already I'm afraid.
> >
> >
> >-----Original Message-----
> >From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf
> >Of Sting
> >Sent: Monday, December 04, 2006 10:18 PM
> >To: namd-l
> >Subject: namd-l: about topology generation
> >
> >Dear all,
> >
> > I want to build the topology of vatamin B12, and I have the
> >topology-tutorial, but I can't find a appropriate template.
> >
> >Does anyone have the similar experience ?
> > Any suggestion will be appreciated.
> >
> > Thank you in advance!
> >
> > Sting
> > stg1979_at_emails.bjut.edu.cn
> > 2006-12-10
>
> = = = = = = = = = = = = = = = = = = = =
>
> Sting
> stg1979_at_emails.bjut.edu.cn
> 2006-12-05
>
>
>

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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