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 - 03:11:39 CDT

Ozlem,

If you already have parameters for both parts of the system (ligand
and protein), then you shouldn't need to make a new prep file. Just
use leap, read in the correct library files, then a .pdb file of the
complex which has atoms and residues labelled to correspond to the
library files, then use leap commands to bond together the correct
two atoms and delete excess atoms.

Dave Evans
London School of Pharmacy

---- 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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