AMBER Archive (2008)

Subject: RE: AMBER: Problems simulating a protein-ligand complex

From: Ross Walker (
Date: Fri Jun 06 2008 - 17:55:37 CDT

Hi Sasha,

I would do something along the lines of the following:

1) open protein pdb in a text editor and remove the END (at the end) and just make sure there is a ter card there. Also remove any connectivity data.

2) open the ligand pdb file and remove anything prior to the first atom definition. Go to the end and remove everything past the last atom definition and just add an END card.

3) cp protein pdb to complex.pdb
   Cat ligand pdb >> complex.pdb

4) load leap
   Source leaprc.ff99SB
   Source leaprc.gaff
   Loadamberprep ligand.prep
   Loadamberparams ligand.frcmod
   Foo = loadpdb complex.pdb
   Solvateoct foo TIP3PBOX 10.0
   Saveamberparm foo prmtop inpcrd

I hope that makes sense and is what you actually want to do I.e make a prmtop and inpcrd for the solvated complex.

All the best

From: [] On Behalf Of Sasha Buzko
Sent: Friday, June 06, 2008 3:16 PM
Subject: Re: AMBER: Problems simulating a protein-ligand complex

Thank you, David.

With hydrogens added in another application, the antechamber part worked.

But another issue appears when I combine the protein structure with the antechamber output in xleap. The ligand is loaded as a prepin file, followed by its frcmod with missing parameters. Then I load the pdb file of the protein and use complex = combine { protein GNP }, where GNP is the name of the residue assigned to the ligand. However, the ligand ends up being shifted in space far from the protein, even though the initial coordinates corresponded to the complex.. I assume that it's the result of the intermediate operations.. but is there a way to combine the two entities into the original complex?

Thanks for any advice


On Fri, 2008-06-06 at 11:59 -0700, David A. Case wrote:

On Fri, Jun 06, 2008, Sasha Buzko wrote:
> The structure has correct connectivity and came directly from a PDB
> file. Since the ligand PDB file is not that large, I'm pasting it below.
> Thank you for any suggestions.

You don't have any hydrogen atoms in your input structure. Antechamber
doesn't know how to add need to draw them in by hand, or
use some other model building program to add all of the hydrogens.

...hope this helps...dac

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