From owner-chemistry@ccl.net Fri Nov 18 07:59:00 2011
From: "Rosana Marques Amorim amorimrm,+,superig.com.br" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: Fragment calculation
Message-Id: <-45897-111117212609-18939-363K16slFY08/Y/ryawORQ(-)server.ccl.net>
X-Original-From: "Rosana Marques Amorim" <amorimrm a superig.com.br>
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Date: Fri, 18 Nov 2011 00:25:57 -0200
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Sent to CCL by: "Rosana Marques Amorim" [amorimrm++superig.com.br]
Partha,

I think you can use onion calculation to do this.

Rosana Amorim

--------------------------------------------------
> From: "Partha P Kundu partha1kundu[A]yahoo.com" <owner-chemistry]^[ccl.net>
Sent: Thursday, November 17, 2011 4:12 PM
To: "Amorim, Rosana " <amorimrm]^[superig.com.br>
Subject: CCL:G: Fragment calculation

>
> Sent to CCL by: "Partha P Kundu" [partha1kundu=-=yahoo.com]
> Dear All,
> I want to optimize a structure with different charge on different parts of 
> system. Is it possible to do in Gaussian 03?
> Thanks in advance.
> Partha.>
>


From owner-chemistry@ccl.net Fri Nov 18 08:34:00 2011
From: "David A. Case case!=!biomaps.rutgers.edu" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: a question about making a parm file containing damino acids with LEaP
Message-Id: <-45898-111117221051-26926-FgBBO3pa2QpcLDeJyx47FA:_:server.ccl.net>
X-Original-From: "David A. Case" <case[-]biomaps.rutgers.edu>
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Date: Thu, 17 Nov 2011 22:10:43 -0500
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Sent to CCL by: "David A. Case" [case- -biomaps.rutgers.edu]
On Thu, Nov 17, 2011, Yawen Li yl6c2|a|mail.missouri.edu wrote:
> 
> 
> I am a beginner of the AMBER program. In the molecule I want to study,
> there is several D amino acids. But it seems to me that "source
> leaprc.ff99SB" do not have any D amino acids. How can I fix this problem
> and generate AMBER topology and coordinate files correctly?

There is no difference in the Amber force field between L- and D-amino acids.
This subject comes up repeatedly on the Amber email reflector, e.g.:

    http://archive.ambermd.org/200809/0155.html

You can find this and other info by going to http://archive.ambermd.org and
typing "d-amino acid" into the search box.

...good luck....dac


From owner-chemistry@ccl.net Fri Nov 18 09:47:01 2011
From: "James McDonagh jm222 . st-andrews.ac.uk" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: IEFPCM non-electrostatics in G09
Message-Id: <-45899-111118094359-20813-9uyTKHvY3WMOF07rWY6eDg],[server.ccl.net>
X-Original-From: "James   McDonagh" <jm222##st-andrews.ac.uk>
Date: Fri, 18 Nov 2011 09:43:56 -0500


Sent to CCL by: "James   McDonagh" [jm222]|[st-andrews.ac.uk]
Dear all, 
              

I am running optimization with IEFPCM and include the non-electrostatic 
contributions using the keywords rep, dis and cav. My questions are;  Are these 
terms contributions included in the optimization process or calculated separately? Secondly is there a way to have their individual contributions or 
total contribution printed in the output?

Thanks in advance, 

James


From owner-chemistry@ccl.net Fri Nov 18 12:51:00 2011
From: "Adam Tenderholt atenderholt+*+gmail.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: Fragment calculation
Message-Id: <-45900-111118123101-1118-rjiNxuItwFaQHg4vf19zBA(-)server.ccl.net>
X-Original-From: Adam Tenderholt <atenderholt:+:gmail.com>
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Date: Fri, 18 Nov 2011 09:30:53 -0800
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Sent to CCL by: Adam Tenderholt [atenderholt ~~ gmail.com]
There's also NWChem, which has implemented the constrained DFT
methodology for this purpose.

Adam


On Thu, Nov 17, 2011 at 10:12 AM, Partha P Kundu
partha1kundu[A]yahoo.com <owner-chemistry---ccl.net> wrote:
>
> Sent to CCL by: "Partha P Kundu" [partha1kundu=-=yahoo.com]
> Dear All,
> I want to optimize a structure with different charge on different parts of system. Is it possible to do in Gaussian 03?
> Thanks in advance.
> Partha.>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>
>