Re: [AMBER] forefile of acetyl coenzyme A

From: <asakiayumikio.gmail.com>
Date: Mon, 07 Mar 2011 06:30:06 -0800 (PST)

dear Ganesh Kamath!


so you mean that i should consider the accoa as a protein?

if there is any refs you could offer, i will be very appreciated!
        2011-03-07
        
        asakiayumikio.gmail.com





发件人:Ganesh Kamath
发送日期:2011-03-07 22:19
收件人:AMBER Mailing List
抄送:
主题: Re: [AMBER] forefile of acetyl coenzyme A
try source leaprc.ff99SB 2011/3/7 <asakiayumikio@gmail.com>: > hello, Ganesh Kamath! > > > sorry, maybe i do not explain the question, > > amber offers the parameters of prep. and frcmod. files > > what i mean is which force field i should use, such as: > > source leaprc.ff99SB > > source leaprc.gaff > > so i question that should i consider the Accoa as the molecular or a protein? > 2011-03-07 > > asakiayumikio@gmail.com > > > > > > 发件人:Ganesh Kamath > 发送日期:2011-03-07 22:11 > 收件人:AMBER Mailing List > 抄送: > 主题: Re: [AMBER] forefile of acetyl coenzyme A > What enzyme is this. If you could share the pdb it would be more useful to see > if there are parameters available in amber. > > > On Mon, Mar 7, 2011 at 9:07 AM, <asakiayumikio@gmail.com> wrote: >> Dear AMBER members, >> >> in a complexes containg an enzyme, a peptide and the accoa >> >> when i load the pdb file into the leap, which forefile should i choose. >> >> leaprc.gaff? or some other forefield? >> >> could anybody doing this job before give me a suggestion? >> >> thank you for your kind help! >> >> >> Best regards >> >> asakiayumikio@gmail.com >> 2011-03-07 >> _______________________________________________ >> AMBER mailing list >> AMBER@ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > . > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Mar 07 2011 - 07:00:04 PST
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