Re: [AMBER] ligand/protein minimization

From: Andrew Olson <>
Date: Mon, 13 Jul 2009 16:53:11 +0100

My apologies,I intially loaded my atp.mol2 file into antechamber and using this protocol from the amber archive used the command
antechamber -i ligand.mol2 -fi mol2 -o ligand.prep -fo prepi -c bcc -rn

parmchk -i ligand.prep -fi prepi -o ligand.frcmod
from here i used the pdb file generated by antechamber (NEWPDB.PDB) and merged it to my protein pdb file. From here i tried loading my prep file for the ligand and the .frcmod file for the ligand as well as my protein/ligand.pdb file. After doing this i used the check command and it gives me that error for the ligand as previously stated and i cannot figure out where i went wrong, or what is giving me the error. As for LeAP, i opened xleap and source. leaprc.99SB and gaff. I think that is all ive done. Thanks for your help and patience.

--- On Sun, 7/12/09, case <> wrote:

From: case <>
Subject: Re: [AMBER] ligand/protein minimization
To: "AMBER Mailing List" <>
Date: Sunday, July 12, 2009, 9:32 PM

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. Here is the error i get after i check the file using
> xleap.FATAL: 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? I will include the pdb file of the ligand
> bound to the protein for reference. 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.


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