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

From: Sangita Kachhap <>
Date: Mon, 09 Sep 2013 12:47:34 +0530



You can use antechamber (amber module) to generate force field library
if you have mol2/pdb file for glycine.

On 2013-09-09 12:24, 张明焜 wrote:

> 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 <> 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? _______________________________________________ AMBER mailing list [1]

Sangita Kachhap
C/O Dr. Balvinder Singh
AMBER mailing list
Received on Mon Sep 09 2013 - 00:30:02 PDT
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