AMBER Archive (2007)

Subject: Re: AMBER: using glycam04 parameters

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Wed Apr 18 2007 - 08:24:38 CDT


You can download the latest glycam04 parameters, and prepfiles from this
website:
http://www.glycam.com/gl_params.html

Also check out this link:
http://www.glycam.com/CCRC/branched_builder.jsp?option=glycam04&option2=FF94

You will be able to build the glycans you want, and download .top/.crd and
leap input files.
Austin-

> On Tue, Apr 17, 2007, Sara Alexandra Moura wrote:
>
>> How can I use the parameters for beta-glucose? Xleap always tels me the
>> parameters for the C1-OH linkage are missing and it does not recognize
>> the
>> OH...
>
> I wonder if the FF parameters for hemiacetals are in GLYCAM FF. It
> might have only FF parameters for Methyl-glycoside derivatives... In
> this case, just pick up the missing FF parameter from GAFF for
> instance, or compute your own FF parameter.
>
> regards, Francois
>
>
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