From owner-chemistry@ccl.net Fri Nov 22 08:34:00 2013
From: "FyD fyd- -q4md-forcefieldtools.org" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python
Message-Id: <-49360-131122040136-7324-Rvk/GIof0+lKu4W83LdwyA[a]server.ccl.net>
X-Original-From: FyD <fyd(~)q4md-forcefieldtools.org>
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Date: Fri, 22 Nov 2013 10:00:09 +0100
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Sent to CCL by: FyD [fyd|*|q4md-forcefieldtools.org]
Dear CCL users,

I am pleased to announce the release of a new q4md-forcefieldtools  
service: R.E.D. Python interfaced by R.E.D. Server Development at  
http://q4md-forcefieldtools.org/REDS-Development/.

R.E.D. Server Development is the Internet service, that provides the  
hardware and software for charge derivation, force field library  
building and force field parameter generation; see  
http://q4md-forcefieldtools.org/REDS-Development/faq.php.

R.E.D. Python is the program, that performs charge derivation, force  
field library building and force field parameter generation. R.E.D.  
Python gives researchers the means to rigorously generate molecular  
electrostatic potential-based empirical force field s for new  
molecules allowing their direct validation and/or use in molecular  
dynamics simulations. In the current release the additive AMBER and  
GLYCAM force field models are fully handled by R.E.D. Python, although  
features related to the non-additive model are already implemented.  
Charge models designed for the OPLS force field and used by CHARMM are  
also available. R.E.D. Python handles force field generation for a  
large ensemble of new molecules and molecular fragments. The approach  
is particularly suited for polymer modeling (biopolymers such as  
proteins, nucleic acids, glyco-conjugates and their bioinorganic  
complexes, as well as functionalized and non-functionalized cabon  
nanotubes). All the elements of the periodic table are handled by the  
service. More generally, the full list of tasks performed by R.E.D.  
Server Development/R.E.D. Python is reported at  
http://q4md-forcefieldtools.org/REDS-Development/news.php.

A demonstration is available from the “Demo” service at the R.E.D.  
Server Development home page; see  
http://q4md-forcefieldtools.org/REDS-Development/RED-Server-demo1.php;  
the data of this demonstration correspond to the R.E.DD.B. project  
available at http://q4md-forcefieldtools.org/REDDB/projects/W-46/.

A new version (version 2.4) of the RESP program is executed, and new  
charge models are proposed based on chemical equivalencing, chemical  
averaging with or without hyperbolic or quadratic restraints; see  
http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php.  
RESP 2.4 can be downloaded at http://q4md-forcefieldtools.org/RED/resp/.

A direct application of the use of R.E.D. Python is the generation of  
the Sanders et al. force field for the peptide nucleic acid  
biopolymer; See http://pubs.acs.org/doi/abs/10.1021/jp4064966 and the  
corresponding project in R.E.DD.B.  
http://q4md-forcefieldtools.org/REDDB/projects/F-93/.

The persons involved in this project are:
   F. Wang: (1)  PhD student & developer of R.E.D. Python
   J.-P. Becker: (1)  Developer of the version 2.4 of RESP
   P. Cieplak: (2)  co-Principal Investigator
   F.-Y. Dupradeau: (1)  co-Principal Investigator
(1) Universite de Picardie Jules Verne, Amiens, France
(2) Sanford | Burnham Medical Research Institute, La Jolla, CA.

The q4md-forcefieldtools project is developed in the context of a  
joined french-USA collaboration between the Universite de Picardie -  
Jules Verne and the Sanford | Burnham Medical Research Institute, and  
is funded by the Conseil Regional de Picardie and the European  
Regional Development Fund.

regards, Francois

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/


From owner-chemistry@ccl.net Fri Nov 22 21:59:00 2013
From: "Bradley Welch bwelch5[-]slu.edu" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: GAMESS submit script for trestles sdsc
Message-Id: <-49361-131122215629-17606-f6k7x300kWBL/VGOOAIVdg(0)server.ccl.net>
X-Original-From: "Bradley  Welch" <bwelch5:slu.edu>
Date: Fri, 22 Nov 2013 21:56:28 -0500


Sent to CCL by: "Bradley  Welch" [bwelch5-,-slu.edu]
Dear all, 

I recently got grant time on trestles and blacklight through xsede. I want to 
run some LMOEDA calculations on GAMESS, but I do not know how to make gamess 
write to the scratch rather than my directroy.  I wanted to know if anyone on 
here uses gamess on trestles and has a queue script they'd be willing to share, 
or help me trouble shoot my current script?  

Bradley Welch 
Saint Louis University