AMBER Archive (2004)

Subject: Re: AMBER: How to covalently bind a ligand to a residue?

From: david.evans_at_ulsop.ac.uk
Date: Fri Aug 06 2004 - 03:22:17 CDT

Ozlem,

Following previous post, I forgot to add that you may find that you
are missing some bonding parameters (angles, dihedrals) in the join
region between the ligand and the tyrosyl. In which case, you need to
choose sensible values for these parameters. One way to do this is to
take them from the gaff force field.
You can then create a frcmod file with these missing parameters and
read these in to leap.

Dave

---- Message from Ozlem Demir <demir_at_qtp.ufl.edu> at 2004-08-05
11:54:19 ------
>
>Hi All,
>
>I wanna combine a sugar ligand to a Tyr residue from its O atom. I
have prep
>file for the ligand from Glycam. I also modified Tyr by deleting the
H of Tyr
>hydroxyl and formed a new prep file for Tyrosyl. Can anybody help me
how to bond
>these covalently and form a new prep file for the ligand bound
Tyrosyl group?
>
>Best,
>
>O.D.
>
>--------------------------------------------------------------------- 

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