Hi,
You could start by creating a PDB file and use R.E.D. Server
See
http://q4md-forcefieldtools.org/REDS/
regards, Francois
> 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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Received on Mon Sep 09 2013 - 03:30:02 PDT
