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
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Sasha Buzko
Sent: Friday, June 06, 2008 3:16 PM
To: amber.scripps.edu
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
Sasha
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 hydrogens...you 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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Received on Sun Jun 08 2008 - 06:08:05 PDT
