Re: [AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file?

From: FyD <>
Date: Fri, 06 Sep 2013 11:51:20 +0200


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 Fri Sep 06 2013 - 03:00:02 PDT
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