Re: [AMBER] parameters for Lys-sugar

From: Lachele Foley (Lists) <"Lachele>
Date: Mon, 23 Apr 2012 16:05:31 -0400

The atom types Francois listed imply using GLYCAM params. You should
use the most recent (06h). Please note that our atom type names have
changed (e.g., CG to Cg). They are now all first-letter upper-case
and the second letter is lower-case. We made the change to be sure
that our params and the protein params, for example, don't overlap.

Yes, leap will tell you which params are missing.

No matter how you determine your parameters, you need to validate
them. Prove that they work for your situation and in the context you
are using them.

I think MMTK might be useful, but I'm not very familiar with what it does.

On Mon, Apr 23, 2012 at 12:26 PM, FyD <> wrote:
> 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:
> # 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
> regards, Francois
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Apr 23 2012 - 13:30:03 PDT
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