On Sat, Sep 26, 2009, Kipras Redeckas wrote:
>
> 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
^^^^^^^
In English, N is "nitrogen", (sodium is "Na").
> creating a bond between them with xleap but that didn't work. The tutorial I
> found here http://ambermd.org/tutorials/advanced/tutorial1/ seems to cope
> with a similar problem but I had no luck in adapting these methods to mine.
Indeed, the tutorial should provide a good pathway. You want to create a
single "residue" that consists of the lysine that has the Schiff base
connection to the retinal -- you don't want two residues (LYS and RET), but
rather one in which the nitrogen-carbon bond is already made. You can then
process this through antechamber.
Beyond that, it's hard to be of much help without knowing more details of what
you actually did.
....dac
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Received on Sat Sep 26 2009 - 07:30:01 PDT
