[AMBER] how to generate a complete amino acid in suitable for the vacuum simulation

From: 张明焜 <zhangmk69.gmail.com>
Date: Wed, 7 May 2014 11:38:49 +0800

Dear professor:

I want to simulate Glycine in vacuum 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 in the shape of solid
powder , so how can I add these two parts to generate a Glycine complete
prmtop file?
Thank you! 

-- 
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ZhangMK
+8623-63063582
Chongqing Institute of Green and Intelligent Technology of Chinese Academy
Sciences.
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Received on Tue May 06 2014 - 21:00:04 PDT
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