Dear Elisa,
> I need protonation state on Serine C-term. I would like to ask you how I can
> do this and there is a good lib that I can use.
The protonation state of the COOH group of Serine does not exist in
solution at pH~7. Thus, a better option to model a neutral Serine
might be to cap it with a NHMe group (NME).
Anyway, if you need this COOH-fragment, you could follow two approaches:
1) The first approach is summarized .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
You follow a similar approach simply replacing MeCOO(-) by MeCOOH
You can find examples of such an approach in R.E.DD.B.; see for instance:
http://q4md-forcefieldtools.org/REDDB/projects/F-41/
Java applet
http://q4md-forcefieldtools.org/REDDB/projects/F-41/JavaApplet-1.php
2) The second approach can be adapted from the 'Central-fragment'
procedure summarized .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
However, you apply a single intra-molecular charge constraint
(INTRA-MCC keyword in a P2N file) on the CH3CO capping group (ACE) and
you do not use any NHMe group:
A single INTRA-MCC set to zero
ACE-NHCH(CH2OH)COOH --> NHCH(CH2OH)COOH
In fact, I would test the case 2) first, and then the case 1)
You also need to decide which phi, psi & chi dihedral angle values you
wish to use to define your conformation(s)...
The whole process can be automatically carried using R.E.D.-III.4 or
R.E.D.Server/R.E.D. IV.
regards, Francois
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Received on Thu Feb 24 2011 - 04:30:09 PST
