AMBER Archive (2009)

Subject: [AMBER] Attaching a ligand to a protein residue.

From: Kipras Redeckas (
Date: Fri Sep 25 2009 - 16:33:58 CDT


I'm currently working on bacteriorhodopsin and I'm having some trouble with
it. I can't seem to find a good way of creating Amber topology and parameter
files of it. Bacteriorhodopsin has its ligand (retinal) covalently bound to
a lysine residue via a Shiff-base link. I extracted the ligand from the pdb
file, added hydrogens to it with Gaussian and used antechamber to create
prep and frcmod files from the Gaussian output. This way retinal simply
appeared as a non-bound residue after I ran xleap. I tried deleting the
excess hydrogens on both sodium (from lysine) and carbon (from retinal) and
creating a bond between them with xleap but that didn't work. The tutorial I
found here seems to cope
with a similar problem but I had no luck in adapting these methods to mine.
Basically the problem is that I need to bind sodium to carbon but both
structures (LYS and RET) end up having extra hydrogens. I'm relatively new
to Amber so I'm still getting the hang of it. I have worked with a protein
that has a non-bound residue in its vicinity but this is something new to
me. I have no idea how to solve this issue and I would appreciate any help.
Thanks in advance.
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