AMBER Archive (2006)

Subject: Re: AMBER: protein ligand complex

From: snoze pa (
Date: Wed Feb 01 2006 - 13:42:11 CST

thanks kara for your reply. I am sure this will help me. I will let you know
once I am done with this.
I have one question after reading your reply. How will u place the ligand
into the original postion. Because the ligand bound to protein is not
accepted in amber. So what I did is to generate same ligand structure with
chemdraw. Now Antechamber is working fine for this ligand. But how to put
this ligand into actual positon. Any answer. thanks a lot for your
reply.keep posting

On 2/1/06, Kara Di Giorgio <> wrote:
> I've done something similar. I used Antechamber to format the ligand
> for import into xLeap. (xLeap will be able to handle the protein as
> long as it doesn't have any non-standard residues.) I loaded gaff.dat
> (to load the .dat file for using antechamber organic molecules) and the
> .prepin and .frcmod file for the ligand in xLeap. I then load the pdb
> with the protein and the ligand together. (The ligand should have the
> same atom names in the pdb as in the output from antechamber.) I'd
> view the unit in xLeap (or save it as a pdb if you're using tleap) to
> make sure everything looks like it should before you continue. You
> should now be able to save the prmtop and inpcrd files needed for amber
> for the complex.
> This all assumes that the ligand is in a binding pocket of some type
> and is not covalently bound. If it is, there's a couple of new steps.
> I've done that, too with DNA and may be able to give you some tips.
> If you have any specific questions, feel free to e-mail me.
> Kara Di Giorgio
> University of the Pacific

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