thank you,
/Urszulla
Urszula Uciechowska, Ph.D.
Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
urszula.uciechowska.chem.umu.se
________________________________________
Von: Lachele Foley (Lists) [lf.list.gmail.com]
Gesendet: Dienstag, 26. Juni 2012 18:56
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for Lys-sugar
I tried to reply to this long ago, but in gmail the "send" button can
end up scrolling behind a button that doesn't send. I just now
noticed and fished it out of my drafts folder. Sorry to be so long.
I've put the new parameters on the site.
On Wed, Apr 25, 2012 at 7:48 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com> wrote:
> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Jun 26 2012 - 11:00:02 PDT
