From owner-chemistry@ccl.net Fri Oct  6 05:50:03 2006
From: "Gilles Marcou gilles.marcou[]pharma.u-strasbg.fr" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: electrostatic potential
Message-Id: <-32723-061006045433-6745-2Ozon3e3d5AZcBjkFLwqEA[]server.ccl.net>
X-Original-From: Gilles Marcou <gilles.marcou^_^pharma.u-strasbg.fr>
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Sent to CCL by: Gilles Marcou [gilles.marcou^^pharma.u-strasbg.fr]
Hello Colette,

in theory, any tool providing Molecular Mechanics calculations is able to do 
that. The main problem you'll have to face is that electrostatic potential of 
proteins is very much related to protein conformations and protonations. This 
means that in order to have scientific ground to your answer, you'll have to 
answer at least those few questions before searching for the right tool:

-which model to use?
-which simulation protocol to use?
-which electrostatic potential is relevent -instantaneous, averaged,long 
distance, etc? 

Now, if all you want is a nice picture, you can always use Tripos's Sybyl with 
biopolymer and molcad extensions. It will provide you with nice 3D 
electrostatic fields lines.

Ciao,
Gilles Marcou

> Hi CCLers,
> I would like to calculate the electrostatic potential of proteins.
> Does anybody know a tool which represents the electrostatic potential of a
> molecule and a tool which calculates this potential starting from a pdb
> file for example? Thanks in advance,
> Colette FOULIE
>
> Laboratoire de Physique, Thorie de la Matire Condense
> CNRS UMR 5027, Universit de Bourgogne.
> 9 avenue Alain Savary
> B.P 47870, F-21078 Dijon Cedex, France
> Tel : 03.80.39.59.50
> Fax: 03.80.39.59.61
>
> colette.foulie[*]u-bourgogne.fr-- 
Gilles Marcou
Université Louis Pasteur de Strasbourg
Institut de Chimie de Strasbourg
4, rue Blaise Pascal
67000 Strasbourg
eMail: g.marcou^^chimie.u-strasbg.fr


From owner-chemistry@ccl.net Fri Oct  6 10:12:00 2006
From: "spitaleri.andrea-#-hsr.it" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: electrostatic potential
Message-Id: <-32724-061005172029-18407-KIZgy792kc6ArT6qtAI3HQ_+_server.ccl.net>
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Sent to CCL by: [spitaleri.andrea(_)hsr.it]



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Hi
what about apbs? you can the visualize the result in vmd and/or pymol
see:
http://apbs.sourceforge.net/

Regards

Andrea

Andrea Spitaleri 
Dulbecco Telethon Institute 
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)

----- Original Message -----
> From: "Nathaniel V. Nucci nvnucci===mail.med.upenn.edu"
<owner-chemistry:+:ccl.net>
Date: Thursday, October 5, 2006 8:54 pm
Subject: CCL: electrostatic potential

> Sent to CCL by: "Nathaniel V. Nucci" [nvnucci|-|mail.med.upenn.edu]
> This is easily done using Qnifft, developed and available free 
> from Dr. Kim
> Sharp's group at University of Pennsylvania.  See:
> http://crystal.med.upenn.edu/software.html 
> to download the program.  The results are readily visualized in 
> PyMol.  
> Cheers,
> Nathaniel
> 
> -- 
> Nathaniel V. Nucci
> Department of Biochemistry and Biophysics
> University of Pennsylvania
> 
> Quoting "Colette FOULIE colette.foulie%x%wanadoo.fr" <owner-
> chemistry- -ccl.net>:
> 
> > Sent to CCL by: "Colette  FOULIE" [colette.foulie..wanadoo.fr]
> > Hi CCLers,
> > I would like to calculate the electrostatic potential of proteins.
> > Does anybody know a tool which represents the electrostatic 
> potential of a
> > molecule and a tool which calculates this potential starting 
> from a pdb file
> > for example?
> > Thanks in advance,
> > Colette FOULIE
> > 
> > Laboratoire de Physique, Thorie de la Matire Condense
> > CNRS UMR 5027, Universit de Bourgogne.
> > 9 avenue Alain Savary
> > B.P 47870, F-21078 Dijon Cedex, France
> > Tel : 03.80.39.59.50
> > Fax: 03.80.39.59.61
> > 
> > colette.foulie[*]u-bourgogne.fr> 
> > 
> > 
> >
> 
> 
> 
> -= This is automatically added to each message by the mailing 
> script =-
> To recover the email address of the author of the message, please 
> changethe strange characters on the top line to the :+: sign. You 
> can also> Conferences: http://server.ccl.net/chemistr
> 
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: 
> search)> 
> RTFI: http://www.ccl.net/chemistr
> 
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
> +-+-+
> 
> 
> 
> 

********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille:+:hsr.it o vai sul sito
www.5xmille.org

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From owner-chemistry@ccl.net Fri Oct  6 12:58:01 2006
From: "Diksha Makwani diksha . iitb.ac.in" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL:G: Gamma calculation in G03
Message-Id: <-32725-061006110249-5935-rcRRmzEPqNgFcY5EVzbQ2Q/./server.ccl.net>
X-Original-From: "Diksha Makwani" <diksha^-^iitb.ac.in>
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Date: Fri, 6 Oct 2006 19:32:31 +0530 (IST)
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Sent to CCL by: "Diksha Makwani" [diksha*_*iitb.ac.in]
Hi CCL users,

I am interested to calculate NLO properties using G03 for some push-pull
molecules.I am giving following keywords in the route section.

# P polar CPHF=RdFreq HF/6-31+G**
For three frequencies 0.07,0.14 and 0.21, this gives me
polarizability(alpha) and first hyperpolarizability(beta) but not second
hyperpol.(gamma).Can anyone tell me how to get gamma from G03 using CPHF.

Also, I wanted to know how to get beta with Density Functional Theory
(DFT) using G03.

Thanks in advance.

Diksha Makwani
diksha[A]iitb.ac.in


From owner-chemistry@ccl.net Fri Oct  6 13:33:00 2006
From: "Jim Kress ccl_nospam-x-kressworks.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: Positive or neutralize?
Message-Id: <-32726-061006111655-9822-8oio1zwKTmLSj3degiNNzg\a/server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam^_^kressworks.com>
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Sent to CCL by: "Jim Kress" [ccl_nospam_-_kressworks.com]
I'm currently doing some QM calculations on water molecules trapped inside a
positively charged cage which, in real life, is surrounded outside the cage
by negative ions (located quite distant from the H2Os, say about 15 - 20
Angstroms, minimum) rendering the entire complex charge neutral.

My specific interest is in the bonding of the waters to various atoms inside
the cage.  All atoms are fixed at their experimental geometry except the
H2Os.  What is the communities opinion about the need to include the
negative charges in the calculations?

All opinions are welcome.

Jim


From owner-chemistry@ccl.net Fri Oct  6 14:09:00 2006
From: "Geoff Skillman skillman .. eyesopen.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: electrostatic potential
Message-Id: <-32727-061006130736-8041-uYiJq6mEfAsf4SDpCfpCXw=server.ccl.net>
X-Original-From: Geoff Skillman <skillman{}eyesopen.com>
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Date: Fri, 06 Oct 2006 10:26:40 -0600
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Sent to CCL by: Geoff Skillman [skillman_._eyesopen.com]
Colette-

VIDA has a 1-button function that calculates the PB electrostatic 
potential around a molecule (protein) using MMFF partial charges.  VIDA 
displays it as either an adjustable isocontour of the potential, or by 
coloring the molecular or accessible surface of the molecule to reflect 
the electrostatic potential at the surface.

VIDA is free for academic use.  see OpenEye (http://www.eyesopen.com) 
for details.

Geoff

spitaleri.andrea-#-hsr.it wrote:
> Sent to CCL by: [spitaleri.andrea(_)hsr.it]
> 
> 
> 
> This is a multi-part message in MIME format.
> 
> ----ba225a5729a6d06
> Content-Type: text/plain; charset=us-ascii
> Content-Disposition: inline
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> 
> Hi
> what about apbs? you can the visualize the result in vmd and/or pymol
> see:
> http://apbs.sourceforge.net/
> 
> Regards
> 
> Andrea
> 
> Andrea Spitaleri 
> Dulbecco Telethon Institute 
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> 
> ----- Original Message -----
> 
>>From: "Nathaniel V. Nucci nvnucci===mail.med.upenn.edu"
> 
> <owner-chemistry ~~ ccl.net>
> Date: Thursday, October 5, 2006 8:54 pm
> Subject: CCL: electrostatic potential
> 
> 
>>Sent to CCL by: "Nathaniel V. Nucci" [nvnucci|-|mail.med.upenn.edu]
>>This is easily done using Qnifft, developed and available free 
>>from Dr. Kim
>>Sharp's group at University of Pennsylvania.  See:
>>http://crystal.med.upenn.edu/software.html 
>>to download the program.  The results are readily visualized in 
>>PyMol.  
>>Cheers,
>>Nathaniel
>>
>>-- 
>>Nathaniel V. Nucci
>>Department of Biochemistry and Biophysics
>>University of Pennsylvania
>>
>>Quoting "Colette FOULIE colette.foulie%x%wanadoo.fr" <owner-
>>chemistry- -ccl.net>:
>>
>>
>>>Sent to CCL by: "Colette  FOULIE" [colette.foulie..wanadoo.fr]
>>>Hi CCLers,
>>>I would like to calculate the electrostatic potential of proteins.
>>>Does anybody know a tool which represents the electrostatic 
>>
>>potential of a
>>
>>>molecule and a tool which calculates this potential starting 
>>
>>from a pdb file
>>
>>>for example?
>>>Thanks in advance,
>>>Colette FOULIE
>>>
>>>Laboratoire de Physique, Thorie de la Matire Condense
>>>CNRS UMR 5027, Universit de Bourgogne.
>>>9 avenue Alain Savary
>>>B.P 47870, F-21078 Dijon Cedex, France
>>>Tel : 03.80.39.59.50
>>>Fax: 03.80.39.59.61
>>>
>>>colette.foulie[*]u-bourgogne.fr> 
>>>
>>>
>>>
>>
>>
>>
>>-= This is automatically added to each message by the mailing 
>>script =-
>>To recover the email address of the author of the message, please 
>>changethe strange characters on the top line to the  ~~  sign. You 
>>can also> Conferences: http://server.ccl.net/chemistr
>>
>>Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: 
>>search)> 
>>RTFI: http://www.ccl.net/chemistr
>>
>>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
>>+-+-+
>>
>>
>>
>>
> 
> 
> ********************************************************************
> Sostieni la ricerca del San Raffaele con il 5permille!
> E' SEMPLICE E NON COSTA NULLA.
> Basta indicare nell'apposito riquadro della dichiarazione dei
> redditi ("Ricerca sanitaria") 
> il codice fiscale della 
> Fondazione Centro S. Raffaele del Monte Tabor:
> 03 06 42 80 153 e ricordarsi di firmare.
> Se vuoi saperne di piu' scrivi a 5permille ~~ hsr.it o vai sul sito
> www.5xmille.org
> 
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> 
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>


From owner-chemistry@ccl.net Fri Oct  6 15:06:00 2006
From: "Dr. Daniel Glossman-Mitnik dglossman]~[gmail.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL:G: Gamma calculation in G03
Message-Id: <-32728-061006141732-10312-2aeQb10ZPiTJxXKXmUXz1g^^^server.ccl.net>
X-Original-From: "Dr. Daniel Glossman-Mitnik" <dglossman:+:gmail.com>
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Sent to CCL by: "Dr. Daniel Glossman-Mitnik" [dglossman(~)gmail.com]
Hi Diksha:

In G03, you must include the keyword  "polar=enonly" if you want to
calculate NLO Properties using DFT.

Best regards,

                                  Daniel  

***********************************************************************
                  Dr. Daniel Glossman-Mitnik
                      Grupo NANOCOSMO - CIMAV
     Química Computacional de Moléculas y Nanomateriales
        Miguel de Cervantes 120 - Comp. Ind. Chihuahua
                  Chihuahua, Chih. 31109 - MEXICO
        Tel.: (52) 614 4391151     FAX: (52) 614 4394852
        Part.: (52) 614 4987113    Cel.: (52) 614 1635322
           E-mail:  daniel.glossman^cimav.edu.mx
                        dglossman^prodigy.net.mx
***********************************************************************
-----Mensaje original-----
De: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] 
Enviado el: Viernes, 06 de Octubre de 2006 11:09 a.m.
Para: Glossman-Mitnik, Daniel 
Asunto: CCL:G: Gamma calculation in G03

Sent to CCL by: "Diksha Makwani" [diksha*_*iitb.ac.in]
Hi CCL users,

I am interested to calculate NLO properties using G03 for some push-pull
molecules.I am giving following keywords in the route section.

# P polar CPHF=RdFreq HF/6-31+G**
For three frequencies 0.07,0.14 and 0.21, this gives me
polarizability(alpha) and first hyperpolarizability(beta) but not second
hyperpol.(gamma).Can anyone tell me how to get gamma from G03 using CPHF.

Also, I wanted to know how to get beta with Density Functional Theory
(DFT) using G03.

Thanks in advance.

Diksha Makwani
diksha(!)iitb.ac.inhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Fri Oct  6 16:09:00 2006
From: "Shobe, David David.Shobe-#-sud-chemie.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: freq=hindrot and near-linear groups
Message-Id: <-32729-061006160735-8434-SZDGs3U9aAzJvi84g0qBkQ**server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe/./sud-chemie.com>
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Sent to CCL by: "Shobe, David" [David.Shobe * sud-chemie.com]
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Is Gaussian03's  freq=3Dhindrot routine able to handle sp-hybridized atoms
and near-linear functional groups?

=20

I was able to calculate the internal rotation energy for propyl-Li and
propyl-BH2 but not propyl-BeH.  I'd like to calculate some propargyl
compounds later.

=20

--David

This e-mail message may contain confidential and / or privileged informatio=
n. If you are not an addressee or otherwise authorized to receive this mess=
age, you should not use, copy, disclose or take any action based on this e-=
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<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:1=
0.0pt;
font-family:Arial'>Is Gaussian03&#8217;s &nbsp;freq=3Dhindrot routine able =
to handle
sp-hybridized atoms and near-linear functional groups?<o:p></o:p></span></f=
ont></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:1=
0.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:1=
0.0pt;
font-family:Arial'>I was able to calculate the internal rotation energy for
propyl-Li and propyl-BH2 but not propyl-BeH.&nbsp; I&#8217;d like to calcul=
ate some
propargyl compounds later.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:1=
0.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span style=3D'font-size:1=
0.0pt;
font-family:Arial'>--David<o:p></o:p></span></font></p>

</div>


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From owner-chemistry@ccl.net Fri Oct  6 21:01:01 2006
From: "Grigori Sigalov sigalov+*+vt.edu" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: electrostatic potential
Message-Id: <-32730-061006033119-23056-60j3y3n6/zGH4K3KkAipdg-x-server.ccl.net>
X-Original-From: Grigori Sigalov <sigalov%vt.edu>
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Date: Thu,  5 Oct 2006 09:49:56 -0500
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Sent to CCL by: Grigori Sigalov [sigalov[*]vt.edu]

VMD calculates (and visualizes!) potential maps:
http://www.ks.uiuc.edu/Research/vmd/
Note that a pdb file does not contain the charges so you would also need a psf
file,
or just use a pqr file. A number of other programs calculate (but don't
visualize)
electrostatic potentials: APBS, DelPhi, PEP, MEAD.

Greg.

Quoting "Colette FOULIE colette.foulie%x%wanadoo.fr" <owner-chemistry%a%ccl.net>:

> Sent to CCL by: "Colette  FOULIE" [colette.foulie..wanadoo.fr]
> Hi CCLers,
> I would like to calculate the electrostatic potential of proteins.
> Does anybody know a tool which represents the electrostatic potential of a
> molecule and a tool which calculates this potential starting from a pdb file
> for example?
> Thanks in advance,
> Colette FOULIE
>
--
Theoretical and Computational Biophysics Group,
Beckman Institute, U of Illinois at Urbana-Champaign