thank you professor,I know your mean about that ,but I am still puzzled
how to carry out that in Amber? Would you please give me a more detailed
explanation?
On Fri, Sep 6, 2013 at 5:51 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Hi,
>
> You need to create a new force field library for Gly - in the neutral
> or in the Zwitterion form...
>
> regards, Francois
>
> > I want to simulate Glycine with amber,what I done like this:
> >
> > tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> >
> > a = sequence{GLY}
> >
> > saveamberparm a gly.prmtop gly.inpcrd
> >
> > but I found that Gly residue in amber is NH-CH2-CO which reduces a -H
> and a
> > -OH compared with the real Glycine like NH2-CH2-COOH, so how can I add
> > these two parts to generate a Glycine complete prmtop file?
>
>
>
>
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>
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ZhangMK
+8623-63063582
Chongqing Institute of Green and Intelligent Technology of Chinese Academy
Sciences.
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Received on Mon Sep 09 2013 - 00:00:03 PDT
