My peptide looks like this HN(-)-CH2-CO-N(-)-CH2-CO-N(-)-CH2-COO(-).
So we can see there are 3 deprotonated N(-) and one COO-. So I want to
develop charge for these amino acid. I know RED I or RED II can develop it.
But I think these three glycines are different. And RED need structure
optimization at first. So I want to know I need to use which structure to do
optimization at first. Just one deprotonated glycine ( -N(-)-CH2-COO(-) or
gly-gly-gly to do optimization at frst.
Thanks,
Jianzhong Liu
Chemistry & Biochemistry
University of Delaware
Newark, DE 19716
Tel: 302-831-3522(O)
---------------------------------------
Vita Brevis, Ars Longa
----- Original Message -----
From: "FyD" <fyd.u-picardie.fr>
To: <amber.scripps.edu>
Sent: Wednesday, March 01, 2006 12:00 AM
Subject: Re: AMBER: How to develop charge for my deprotonated glycine
> Quoting Jianzhong Liu <zhong.udel.edu>:
>
>> 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:
> http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-15/info.html
> N-terminal neutral fragment of O-methyl-L-tyrosine:
> http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-37/info.html
>
> To get all the files and RESP inputs required use the download section of
> R.E.DDB.: http://www.u-picardie.fr/labo/lbpd/REDDB/ "-- Molecule keyword"
> =
> NH2-terminal
>
> 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 http://www.u-picardie.fr/labo/lbpd/RED/, 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 http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#27
>
> regards, Francois
>
>
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Received on Sun Mar 05 2006 - 06:10:19 PST
