AMBER Archive (2008)

Subject: Re: AMBER: drug/protein interaction modeling setup

From: Sean Johnston (sean.johnst_at_gmail.com)
Date: Fri Oct 31 2008 - 14:31:56 CDT

Just to inform of the way I found to deal with this problem. Basically, my
the ligand in my protein/ligand setup does not have atom types.

1. Extract ligand and protein coordinates separately in pdb (can use mol2).
--> ligand.pdb, protein.pdb

2. In sleap
>LIG = loadpdb ligand.pdb
>fixbond LIG
>addhydr LIG
>savemol2 LIG ligand.mol2

3. Using antechamber:
>antechamber -i ligand.pdb -fi pdb -o ligand+types.mol2 -fo mol2 -c bcc
-s 2

4. In tleap
>LIG = loadmol2 ligand+types.mol2
>PROT = loadpdb protein.pdb
>COMP = combine { LIG PROT }

fixbond and addhydr seem to work fine in the adding of the hydrogens. Since
antechamber can export as a mol2, we avoid the internal coordinates of the
prepi, and original coordinates are conserved.

Thanks to all who helped me out here!

-Sean

Sean Johnston
johnstos_at_stolaf.edu
sean.johnst_at_gmail.com

On Mon, Oct 20, 2008 at 5:39 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:

> Once you have a prepin, the secret is to load it and then load your
> pdb with protein and ligand coordinates. These pdb coordinates will
> be applied to all residues, so the relative locations of protein and
> ligand will be preserved. Ultimately the whole system will be shifted
> when you solvate it, so do not get too attached to the coords in the
> pdb.
>
> Bill
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