[AMBER] how to use commands “sequence”, “set”, “add”, “bond”, “ impose” or someothers necessary to add a –H and a –OH to the GLY

From: (wrong string) 张明焜 <zhangmk69.gmail.com>
Date: Tue, 24 Sep 2013 14:53:36 +0800

Hello Professor:

     I want to get the prmtop and inpcrd files of Glycine, what I done like

tleap –s –f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

a = sequence{GLY}

saveamberparm a gly.prmtop gly.inpcrd

but result get from above is NH-CH2-CO which reduces a -H and a -OH
compared with the real Glycine like NH2-CH2-COOH.

I have read “Chapter LEaP” in AmberTool12 Nowadays,I found LEaP can only
add a -C or -N atom in front or end of the GLY, but how can I add a –H and
a –OH? can I use the commands “sequence”, “set”, “add”, “bond”, “ impose”
or someothers necessary to accomplish this task?
Thank you !

Chongqing Institute of Green and Intelligent Technology of Chinese Academy
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Received on Tue Sep 24 2013 - 00:00:02 PDT
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