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

From: (wrong string) 张明焜 <zhangmk69.gmail.com>
Date: Fri, 6 Sep 2013 17:23:27 +0800

Dear professor:

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?
Thank you!


Chongqing Institute of Green and Intelligent Technology of Chinese Academy
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Received on Fri Sep 06 2013 - 02:30:02 PDT
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