From owner-chemistry@ccl.net Fri Jan 20 14:15:01 2017
From: "Fenley, Andrew afenley^^ucsd.edu" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL:G: ONIOM Calculations (Protein-Ligand)
Message-Id: <-52607-170120132220-11837-/5cprXglIVYiTskttqiZwg^^server.ccl.net>
X-Original-From: "Fenley, Andrew" <afenley+*+ucsd.edu>
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Date: Fri, 20 Jan 2017 18:22:13 +0000
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Sent to CCL by: "Fenley, Andrew" [afenley*_*ucsd.edu]
Hello,
 
I am trying to setup 3-layer ONIOM calculations for a protein-ligand binding site within Gaussian G09 RevE. The high layer contains the ligand and any whole residue within 3 Angstroms of the ligand. The medium layer is any whole residue within 5 Angstroms of the ligand that has not been included in the high layer. And the low layer consists of everything else. The layer models are: B3LYP (6-31G*):PM6:AMBER. One issue I keep running into with regards to optimization is that if I specify the ligand to be a ‘frozen’ block (by setting -2 in the appropriate field per atom), then I get an error saying the default optimizer supports only 1 rigid structure.
 
Ideally, what I want to do is, let all hydrogens of the protein (in any layer) optimize, along with the ligand optimizing its location within the binding site as a rigid block (so just translation / rotation effectively of the whole molecule). And the rest of the atomic coordinates of the system stay frozen (fixed to the original input coordinates). I thought the way to do this would be to specify ‘0’ for all Hydrogens, ‘-2’ for the ligand, and ‘-1’ for everything else per input line describing each atom right after the element-type-charge column. Attempts to use other options to the optimizer like Opt=QuadMacro did not help.

Additional details:
The atoms in the input file are represented using cartesian coordinates. Geom=connectivity is used, and all the bonding information is provided. Additional vdW parameters for the ligand are also provided in the input file (taken from GAFF). Partial charges are provided per atom with EmbedCharge set in the header of the input file. 
 
Thank you for your help!
Andrew
afenley*o*vt.edu


From owner-chemistry@ccl.net Fri Jan 20 16:02:01 2017
From: "Andrew Jackson andrew.jackson- -solvay.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: ideas for data sharing and a project assessment tool
Message-Id: <-52608-170120160027-16001-mDV4I6/1+5HZmMjumcl/rQ++server.ccl.net>
X-Original-From: "Andrew  Jackson" <andrew.jackson-x-solvay.com>
Date: Fri, 20 Jan 2017 16:00:26 -0500


Sent to CCL by: "Andrew  Jackson" [andrew.jackson|*|solvay.com]
Hello!

The modeling group I started last year is seeking to become more organized 
in 2017. 

Does anyone have experience with perhaps a tool to rank the modeling 
project requests in an industrial setting, or with effective ways to 
catalog and disseminate results from atomistic simulations?

Thanks!

Andrew Jackson