AMBER Archive (2009)

Subject: Re: [AMBER] ligand/protein minimization

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Jul 12 2009 - 21:32:29 CDT

On Fri, Jul 10, 2009, Andrew Olson wrote:

> When trying to minimize my protein with ligand bound (directly from
> antechamber) it keeps throwing up errors in xleap (after check) that
> something is wrong with my ligand atom types, but i cant seem to
> figure it out. Â Here is the error i get after i check the file using
> xleap.FATAL: Â Atom .R<SUB 189>.A<O17 1> does not have a type.I also
> have a clash with ligand and a residue in the protein, will that be a
> problem for minimizing? Â I will include the pdb file of the ligand
> bound to the protein for reference. Â I want to keep the ligand there,
> even with the clash, in hopes that the minimzing will move the domain
> out of the way.

You need to provide much more information about your ligand. Just saying
"directly from antechamber" is a little vague. Most often, having an atom
without a type means that you loaded a pdb file (or mol2 file, or something
with coordinates) whose names don't match those in the library you created
for the "SUB" residue. But without knowing either (a) what antechamber
commands you used; and (b) what LEaP commands you used, it's pretty much
impossible to help much.

...dac

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