Re: AMBER: How to develop charge for my deprotonated glycine

From: FyD <>
Date: Wed, 01 Mar 2006 06:00:37 +0100

Quoting Jianzhong Liu <>:

> I just want to run a simulation about deprotonated glycine. How can I
> develop the charge for it by using RESP?

What do you mean by deprotonated glycine ? Do you mean the uncharged N-terminal
fragment of glycine ?
i. e. NH2-CH2-CO

- If so, you could follow:
N-terminal neutral fragment of alpha-aminoisobutyric acid:
N-terminal neutral fragment of O-methyl-L-tyrosine:

To get all the files and RESP inputs required use the download section of
R.E.DDB.: "-- Molecule keyword" =

This has been done using 2 molecules Me-NH2 + ACE-AA-NME in RESP charge
derivation, using one inter-molecular charge restraint = 0 between Me (of
Me-NH2) and ACE-NH of ACE-AA-NME and using one intra-molecular restraint = 0
for NME of ACE-AA-NME...

- May be it would be more simple to use a single molecule NH2CH2CO-NME and using
one intra-molecular restraint = 0 for NME of ACE-AA-NME...

All is done automatically in R.E.D. III, still fighting with the tutorial...
Concerning R.E.D. II, you have to
proceed in two steps (1- run R.E.D. II without constraint and 2- add the
intra/inter-molecular charge restraint in the RESP input1 generated and re-run
the fit) See

regards, Francois

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Received on Sun Mar 05 2006 - 06:10:11 PST
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