AMBER Archive (2009)

Subject: Re: [AMBER] ligand/protein minimization

From: Andrew Olson (
Date: Mon Jul 13 2009 - 12:10:18 CDT

Just incase anyone else has this problem, the coordinates for NEWPDB.PDB have the same name as that of the prep file but the coordinates are different so if you make the coordinates the same in the prep file as taht of the PDB file, it will work. †Thanks for your help dac.

--- On Mon, 7/13/09, case <> wrote:

From: case <>
Subject: Re: [AMBER] ligand/protein minimization
To: "AMBER Mailing List" <>
Date: Monday, July 13, 2009, 11:29 AM

On Mon, Jul 13, 2009, Andrew Olson wrote:

> 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

I'm not sure what is supposed to be in NEWPDB.PDB -- I've never used that
myself.† Are the atom names in NEWPDB the same ones as in "ligand.prep",
especially atom O17?

Basically, you can probably use the orginal pdb file (without hydrogens, etc.)
as long as you modify it so that the names in the pdb file exactly match the
names in the ligand.prep file.

...hope this helps....dac

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