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

From: Jason Swails <>
Date: Tue, 24 Sep 2013 07:04:52 -0400

On Tue, Sep 24, 2013 at 2:53 AM, 张明焜 <> wrote:

> Hello Professor:
> I want to get the prmtop and inpcrd files of Glycine, what I done like
> this:
> tleap –s –f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> a = sequence{GLY}

This is an 'internal' glycine that expects an amino acid on both the
N-terminal and C-terminal sides (as you found out, it is missing the second
carboxylate oxygen and hydrogens on the N-terminus). There are C-terminal
(with COO- groups at the carboxylate end) and N-terminal (with NH3+ groups
at the N-terminal end) available in Amber, but they still expect a residue
at the non-terminal end. Amber does not have any 'pure' amino acids in its
residue libraries -- you would have to build your own.

> 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.

It may seem like a nitpick, but unless you are simulating in the gas phase,
'real Glycine' is never neutral at both termini. At high pH it is
NH2-CH2-COO-​​, at low pH it is NH3+--CH2--COOH, and at neutral pHs it is
in its zwitterionic form NH3+--CH2--COO-. Given this realization, you
should choose a model that best represents the conditions you want to
simulate. In any case, you will have to build the appropriate residue
(Amber programs may not be the best equipped programs to do this) and
derive charges for it (with programs like antechamber or R.E.D.) as well as
the bonded parameters.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 24 2013 - 04:30:03 PDT
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