From: John E. Kerrigan <kerrigje.UMDNJ.EDU>
Date: Tue, 17 Apr 2007 08:40:54 -0400

Any text editor (nedit, jot, etc) will suffice. Copy and paste the pdb
coordinates you used as input for antechamber into the end of your
receptor file (assuming your ligand has been pre-docked either by a
docking program or manually). Be certain sure that the "TER" cards are
in place at the end of each chain (i.e. protein & ligand). You do not
need the "CONECT" records as the prep file you prepared with antechamber
will take care of connectivity for the ligand. In fact, I remove all of
the "CONECT" records from my pdb files before processing with Leap as
the "CONECT" records sometimes confuse Leap.

Be careful using Sybyl. Always use "center view" when loading files
into Sybyl. Otherwise Sybyl will change the coordinates of your file to
fit its reference frame.



Beale, John wrote:
> I am trying to create the files of a ligand bound to a protein for
> xleap. I have successfully used Antechamber to generate the prmtop and
> inpcrd files, plus a pdb, for my ligand. I have the pdb file of the
> protein. My question is this: how do I merge the two files so that the
> ligand becomes associated with the correct site on the protein? If I use
> Sybyl to generate a pdb file of the complex, I assume that I will
> somehow have to replace the content in the Sybyl pdb file with the
> antechamber content. I guess what I am trying to ask in a roundabout way
> is how do I build a pdb file of a complex using a ligand from
> antechamber and the pdb file of the protein?
> John Beale

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Received on Wed Apr 18 2007 - 06:07:29 PDT
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