Re: [AMBER] parameters for Lys-sugar

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Mon, 23 Apr 2012 18:26:41 +0200

Dear Urszula,

> I run RED to get the resp charges for my Lys-sugar molecule which I
> will later add to the peptide (see attachment). Now I need to
> generate parameters however I dont really know how to start it ? is
> there any tutoraial for that? what force field should I use?

- you first need to add the FF atom types in the mol2 file.
See for instance the script1.ff file in a R.E.DD.B. project:
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff

# set FF atom types
set MGR.1.C1 type CG
set MGR.1.H1 type H2
set MGR.1.O1 type OS
set MGR.1.C2 type CG
set MGR.1.H2 type H1
# etc...

- then, you can run LEaP to determine which FF parameters are missing...

- finally, you could generate a phi, psi map by QM and MM to compare
QM vs MM...
   See for instance
http://onlinelibrary.wiley.com/doi/10.1002/jcc.21099/abstract

regards, Francois



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Received on Mon Apr 23 2012 - 09:30:02 PDT