Lachele,
where can we download the GLYCAM06h files? Here, the latest version is
06g-1:
http://glycam.ccrc.uga.edu/ccrc/pages/parameters.html
Thanks,
Jan-Philip
On 04/23/2012 10:05 PM, Lachele Foley (Lists) wrote:
> 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<fyd.q4md-forcefieldtools.org> 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:
>> 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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>
>
>
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Received on Wed Apr 25 2012 - 05:00:03 PDT
