On Sep 27, 2011, at 2:34 PM, Yao Yao wrote:
> Hi,
>
> I am going to build a structure file for Green Fluorescent Protein (GFP) chromophore from scratch and run simulation in Amber.
> Since its structure is not embedded in Amber ff, I was wondering if xLeap can do it or I need to refer to other software.
> Anyone has any experience in constructing this kind of molecules?
> Thanks,
>
> Yao Yao
>
Xleap GUI will help if you need to fix the covalent structure or add
hydrogens. Other than that you need to generate a new residue
description. See the tutorials on the AMBER web site and/or Google
for "RED Server".
IIRC (from the deep dark past) GFP chromophore is a modified amino
acid, correct? I would take the structure from a crystal structure
of the protein (just edit away all the rest of the protein in a text
editor.) Then you need to use antechamber or RED to generate the
partial charges.
See the email list archives of the past 2 weeks; there has been quite
a lot of email list activity about doing things like this in that
time frame.
Good luck,
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Tue Sep 27 2011 - 13:00:04 PDT
