From owner-chemistry@ccl.net Tue Nov  8 08:33:00 2005
From: "yang zhen na yangzn553,;,nenu.edu.cn" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: proton transfer
Message-Id: <-29897-051108083131-4022-qFPYIieeMPFYSyIpnzYiAQ _ server.ccl.net>
X-Original-From: "yang zhen na" <yangzn553*nenu.edu.cn>


Sent to CCL by: "yang zhen na" [yangzn553-$-nenu.edu.cn]
can intramolecular proton transfer reaction happen in the Franck-condon geometry in the excited state? that is to say the reaction happen as the molecular get to the excited state before relaxation.


From owner-chemistry@ccl.net Tue Nov  8 09:08:00 2005
From: "kiruba sebastina vaji772002 . yahoo.co.in" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL:G: Ab initio calculations in presence of an electric field
Message-Id: <-29898-051108002158-15746-WmjhO1gXdqcNI6R0gik6bw+*+server.ccl.net>
X-Original-From: kiruba sebastina <vaji772002^-^yahoo.co.in>
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Sent to CCL by: kiruba sebastina [vaji772002 ~~ yahoo.co.in]
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Hi,
 
Is it possible to perform ab initio calculations in the presence of an electric field using the Gaussian program? If yes, could you please elaborate it.
 
Thank You!
 
Regards,
Kiruba.


		
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 Enjoy this Diwali with Y! India Click here
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<DIV>
<DIV><FONT face=courier color=#0000ff size=4>Hi,</FONT></DIV>
<DIV><FONT face=Courier color=#0000ff size=4></FONT>&nbsp;</DIV>
<DIV><FONT face=Courier color=#0000ff size=4>Is it possible to perform ab initio calculations in the presence of an electric field using the Gaussian program? If yes, could you please elaborate it.</FONT></DIV>
<DIV><FONT face=Courier color=#0000ff size=4></FONT>&nbsp;</DIV>
<DIV><FONT face=Courier color=#0000ff size=4>Thank You!</FONT></DIV>
<DIV><FONT face=Courier color=#0000ff size=4></FONT>&nbsp;</DIV>
<DIV><FONT face=Courier color=#0000ff size=4>Regards,</FONT></DIV>
<DIV><FONT face=Courier color=#0000ff size=4>Kiruba.</FONT></DIV></DIV><p>
		<hr size=1> 
Enjoy this Diwali with Y! India <a href="http://in.promos.yahoo.com/fabmall/index.html">Click here</a>
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From owner-chemistry@ccl.net Tue Nov  8 09:43:00 2005
From: "kawai Chan kawai^liua2.chem.cuhk.edu.hk" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL:G: Format of Cube file generated by Gaussian
Message-Id: <-29899-051108002147-15633-6YQGuNTd38amvVfJrfn5YQ+*+server.ccl.net>
X-Original-From: "kawai  Chan" <kawai[*]liua2.chem.cuhk.edu.hk>


Sent to CCL by: "kawai  Chan" [kawai]-[liua2.chem.cuhk.edu.hk]
Dear all,
I'm calculating some systems with a singly occupied molecular orbital
(SOMO). In order to figure out the center of the unpaired electron,
therefore, i have to calculate the electron density at each grid points.
I have used Gaussian with the following option after calculation of the
Single point energy.

Cube(40,orbit) Density=checkpoint Geom=allcheck Guess=(Read,Only)

mg-6nh3-b3-1-i1.cube
HOMO

and the output of mg-6nh3-b3-1-i1.cube:
 Trimer
 SCF Molecular Orbitals
  -25  -14.548373  -12.000272  -10.882064
   41    0.626953    0.000000    0.000000
   39    0.000000    0.626953    0.000000
   39    0.000000    0.000000    0.626953
   12   12.000000   -2.547857    0.000244    1.118452
    7    7.000000   -6.774728    0.000564    1.197873
    7    7.000000   -1.766518   -3.163418   -1.412186
    7    7.000000   -1.765943    3.162334   -1.413966
    7    7.000000    3.833404   -3.637069   -1.536647
    7    7.000000    3.833884    3.638677   -1.533802
    1    1.000000   -7.732022    0.000449   -0.480774
    1    1.000000   -7.405326   -1.533801    2.185436
    1    1.000000   -7.405106    1.535233    2.185102
    1    1.000000   -2.448998   -3.063773   -3.215833
    1    1.000000   -2.446611    3.060669   -3.218186
    1    1.000000   -2.404312   -4.839008   -0.699176
    1    1.000000   -2.405324    4.838241   -0.703121
    1    1.000000    0.195536   -3.360386   -1.562601
    1    1.000000    0.196148    3.360203   -1.562675
    1    1.000000    4.708919   -3.327432   -3.221695
    1    1.000000    4.710781    3.331691   -3.218617
    1    1.000000    4.378661   -5.392139   -0.964945
    1    1.000000    4.377670    5.393355   -0.959501
    1    1.000000    4.558482   -2.373532   -0.264542
    1    1.000000    4.558838    2.374000   -0.262770
    7    7.000000    5.345309   -0.001378    3.321842
    1    1.000000    3.615309   -0.000563    4.175061
    1    1.000000    6.292775    1.530782    4.003096
    1    1.000000    6.291006   -1.534881    4.002531
    2  36  262
  5.90704E-06  4.25632E-07  7.23360E-06  5.10726E-07  8.75594E-06 
6.05206E-07
  1.04765E-05  7.08192E-07  1.23906E-05  8.18276E-07  1.44857E-05 
9.33502E-07
  1.67400E-05  1.05138E-06  1.91225E-05  1.16896E-06  2.15927E-05 
1.28289E-06
  2.41017E-05  1.38957E-06  2.65928E-05  1.48534E-06  2.90041E-05 
1.56662E-06
  3.12700E-05  1.63011E-06  3.33245E-05  1.67302E-06  3.51040E-05 
1.69317E-06
  3.65507E-05  1.68920E-06  3.76153E-05  1.66065E-06  3.82599E-05 
1.60802E-06
  3.84606E-05  1.53276E-06  3.82089E-05  1.43724E-06  3.75124E-05 
1.32462E-06
  3.63945E-05  1.19868E-06  3.48933E-05  1.06361E-06  3.30595E-05 
9.23808E-07
  3.09530E-05  7.83595E-07  2.86397E-05  6.47027E-07  2.61883E-05 
5.17684E-07
  2.36662E-05  3.98514E-07  2.11370E-05  2.91736E-07  1.86578E-05 
1.98788E-07
  1.62774E-05  1.20341E-07  1.40353E-05  5.63584E-08  1.19611E-05 
6.19805E-09
  1.00746E-05 -3.12594E-08  8.38660E-06 -5.74699E-08  6.89987E-06
-7.40865E-08
  5.61026E-06 -8.28331E-08  4.50820E-06 -8.53972E-08  3.58007E-06
-8.33481E-08

May i ask :
1) are these values are the coefficents of  the 36th and  262th MO in each
grid point?
2) can i obtained the density at each grid points of the 36th MO by take
square of the values??

Thanks!!!


From owner-chemistry@ccl.net Tue Nov  8 10:18:00 2005
From: "Pradipta Bandyopadhyay pradipta .. iitg.ernet.in" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: using DELPHI with g77 and gcc !
Message-Id: <-29900-051108082410-790-K8TqRzRDkxFz0ZdCcmUZDw-,-server.ccl.net>
X-Original-From: Pradipta Bandyopadhyay <pradipta*o*iitg.ernet.in>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Tue, 8 Nov 2005 17:18:44 +0530 (IST)
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Sent to CCL by: Pradipta Bandyopadhyay [pradipta:+:iitg.ernet.in]
Has anyone used DELPHI (from Barry Honig's group) with  g77 and gcc 
compiler in red hat linux? I learned that pg77 and pgcc are the default 
compilers for DELPHI - but these are not free.

thanks.

    Pradipta


From owner-chemistry@ccl.net Tue Nov  8 10:53:00 2005
From: "Stouten, Pieter Nervianoms Pieter.Stouten%a%nervianoms.com" <owner-chemistry,;,server.ccl.net>
To: CCL
Subject: CCL: how to find active site?
Message-Id: <-29901-051108064102-20005-qZF9i8vFg9E/WadEosbEPg,;,server.ccl.net>
X-Original-From: "Stouten, Pieter [Nervianoms]" <Pieter.Stouten]_[nervianoms.com>
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Sent to CCL by: "Stouten, Pieter [Nervianoms]" [Pieter.Stouten-,-nervianoms.com]
Hello Steven,

You could try PASS (Putative Active Sites with Spheres):

<http://www.ccl.net/cca/software/UNIX/pass/overview.shtml>

As far as I know, it is the fastest and (maybe with the exception of Ajay Jain's) the best active site finder.

Good luck,

Pieter

Pieter F.W. Stouten, Ph.D.
Sr. Research Advisor and Head, Molecular Modelling & Design
Nerviano Medical Sciences, Nerviano (Mi), Italy


-----Original Message-----
> From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net]
Sent: Saturday, November 05, 2005 3:11 AM
To: Stouten, Pieter [Nervianoms]
Subject: CCL: how to find active site?


Hi, Everyone!
  
  I will very appreciate if somebody lets me know how to find an active site
> from a protein-ligand structure?
  Thank you!

Steven


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From owner-chemistry@ccl.net Tue Nov  8 11:28:00 2005
From: "Zhao Yuan ccl#mail.sioc.ac.cn" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: how to find active site?
Message-Id: <-29902-051108023042-14788-oj7Mg8XXulgAHnqT96mKKw * server.ccl.net>
X-Original-From: "Zhao Yuan" <ccl-*-mail.sioc.ac.cn>
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Sent to CCL by: "Zhao Yuan" [ccl*_*mail.sioc.ac.cn]

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Thank you very much! =0D
 =0D
-------Original Message-------=0D
 =0D
> From: Monika Rella bmbmre(!)bmb.leeds.ac.uk=0D
Date: 11/08/05 03:57:36=0D
To: Wang, Renxiao =0D
Subject: CCL: how to find active site?=0D
 =0D
Sent to CCL by: Monika Rella [bmbmre],[bmb.leeds.ac.uk]=0D
Hi Steven,=0D
 =0D
One of my colleagues wrote a piece of software (an energy based method) t=
hat=0D
helps you to quickly identify the active site on a protein in absence of =
a=0D
bound ligand. You just need to upload your protein structure at=0D
http://www.bioinformatics.leeds.ac.uk/qsitefinder/=0D
 =0D
Hope that may be useful!=0D
 =0D
Monika=0D
 =0D
 =0D
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<DIV>Sent to CCL by: Monika Rella [bmbmre],[bmb.leeds.ac.uk]</DIV>
<DIV>Hi Steven,</DIV>
<DIV>&nbsp;</DIV>
<DIV>One of my colleagues wrote a piece of software (an energy based meth=
od) that</DIV>
<DIV>helps you to quickly identify the active site on a protein in absenc=
e of a</DIV>
<DIV>bound ligand. You just need to upload your protein structure at</DIV=
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From owner-chemistry@ccl.net Tue Nov  8 12:02:01 2005
From: "Theo de Bruin theodorus.de-bruin!^!ifp.fr" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL:G: transition state searches with CASSCF ???
Message-Id: <-29903-051108092752-12299-aH2zRFBrqiFkd9P2SSSQEg()server.ccl.net>
X-Original-From: "Theo de Bruin" <theodorus.de-bruin^ifp.fr>


Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin%a%ifp.fr]
Hello 

I wish to know whether it is possible to perform transition state searches at the CASSCF level of theory using Gaussian 03 rev C02. I asked the same question to the helpdesk of Gaussian but I gave up, after waiting more than 5 weeks. 
I would like to study a bi-molecular reaction in which two (neutral) molecules are transformed into two radicals (reversed dismutation reaction). 
Neither B3LYP nor X3LYP are capable to locate the TS, while unrestricted MP2 gives the correct TS but unusual high barrier (delta H activation) and delta H are obtained.

Thanks for sharing your thoughts how to handle this problem.

Kind regards,

Theo de Bruin
theodorus.de-bruin#,#ifp.fr


From owner-chemistry@ccl.net Tue Nov  8 12:38:01 2005
From: "Shobe, David dshobe||sud-chemieinc.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL:G: Ab initio calculations in presence of an electric field
Message-Id: <-29904-051108100746-9668-kc3HqW59mMwSJpvAgqos6Q/a\server.ccl.net>
X-Original-From: "Shobe, David" <dshobe!^!sud-chemieinc.com>
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Sent to CCL by: "Shobe, David" [dshobe__sud-chemieinc.com]
Read the section on the "Field" keyword in the manual.  You can do some types of calculations, but not others. 

--David Shobe, Ph.D., M.L.S.
Süd-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.
 

-----Original Message-----
> From: owner-chemistry(0)ccl.net [mailto:owner-chemistry(0)ccl.net] 
Sent: Tuesday, November 08, 2005 9:12 AM
To: Shobe, David
Subject: CCL:G: Ab initio calculations in presence of an electric field

Sent to CCL by: kiruba sebastina [vaji772002 ~~ yahoo.co.in]
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Content-Type: text/plain; charset=iso-8859-1
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Hi,
 
Is it possible to perform ab initio calculations in the presence of an electric field using the Gaussian program? If yes, could you please elaborate it.
 
Thank You!
 
Regards,
Kiruba.


		
---------------------------------
 Enjoy this Diwali with Y! India Click here
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<DIV>
<DIV><FONT face=courier color=#0000ff size=4>Hi,</FONT></DIV> <DIV><FONT face=Courier color=#0000ff size=4></FONT>&nbsp;</DIV> <DIV><FONT face=Courier color=#0000ff size=4>Is it possible to perform ab initio calculations in the presence of an electric field using the Gaussian program? If yes, could you please elaborate it.</FONT></DIV> <DIV><FONT face=Courier color=#0000ff size=4></FONT>&nbsp;</DIV> <DIV><FONT face=Courier color=#0000ff size=4>Thank You!</FONT></DIV> <DIV><FONT face=Courier color=#0000ff size=4></FONT>&nbsp;</DIV> <DIV><FONT face=Courier color=#0000ff size=4>Regards,</FONT></DIV> <DIV><FONT face=Courier color=#0000ff size=4>Kiruba.</FONT></DIV></DIV><p>
		<hr size=1>
Enjoy this Diwali with Y! India <a href="http://in.promos.yahoo.com/fabmall/index.html">Click here</a>
--0-1516630953-1131423708=:74145--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. 
Thank you.


From owner-chemistry@ccl.net Tue Nov  8 13:50:01 2005
From: "David F. Green dfgreen[]ams.sunysb.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: using DELPHI with g77 and gcc !
Message-Id: <-29905-051108133629-16252-mQgbazzxsHxkiqSAsLLzkw---server.ccl.net>
X-Original-From: "David F. Green" <dfgreen*ams.sunysb.edu>
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Sent to CCL by: "David F. Green" [dfgreen[a]ams.sunysb.edu]
IIRC, g77/gcc gives errors on the memory allocation code in DelPhi 
(although I'm not positive on whether this is still the case in the 
newer versions).

If you will be unning under Linux on x86 architecture (Intel or AMD), I 
would suggest using Intel's compilers (free for non-commerical use):

http://www.intel.com/cd/software/products/asmo-na/eng/compilers/flin/219771.htm

DelPhi does compile with them (I don't recall if any tricks are needed - 
but I don't think so), and they produce good, fast code.

Hope this helps.

========================================================================
David F. Green                                  <dfgreen#ams.sunysb.edu>
  Assistant Professor                 http://www.ams.sunysb.edu/~dfgreen/
  Applied Mathematics and Statistics
  Stony Brook University                          Office: +1-631-632-9344
  Math Tower, Room 1-117                          Mobile: +1-617-953-3922
  Stony Brook, NY 11794-3600                         Fax: +1-631-632-8490
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Pradipta Bandyopadhyay pradipta .. iitg.ernet.in wrote:
> Sent to CCL by: Pradipta Bandyopadhyay [pradipta:+:iitg.ernet.in]
> Has anyone used DELPHI (from Barry Honig's group) with  g77 and gcc 
> compiler in red hat linux? I learned that pg77 and pgcc are the default 
> compilers for DELPHI - but these are not free.
> 
> thanks.
> 
>     Pradipta> 
> 
>


From owner-chemistry@ccl.net Tue Nov  8 17:38:00 2005
From: "Wai-To Chan chan!=!curl.gkcl.yorku.ca" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL:G: transition state searches with CASSCF ???
Message-Id: <-29906-051108170010-20338-EQwFv3o0Kmc6bEgkcRRNCg###server.ccl.net>
X-Original-From: Wai-To Chan <chan:-:curl.gkcl.yorku.ca>
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Sent to CCL by: Wai-To Chan [chan]-[curl.gkcl.yorku.ca]
<<<<<<<
I wish to know whether it is possible to perform transition state searches at the CASSCF level of theory using Gaussian 03 rev C02. I asked the same question to the helpdesk of Gaussian but I gave up, after waiting more than 5 weeks. 
I would like to study a bi-molecular reaction in which two (neutral) molecules are transformed into two radicals (reversed dismutation reaction). 
Neither B3LYP nor X3LYP are capable to locate the TS, while unrestricted MP2 gives the correct TS but unusual high barrier (delta H activation) and delta H are obtained.

Thanks for sharing your thoughts how to handle this problem.

Kind regards,

Theo de Bruin
theodorus.de-bruin#,#ifp.fr
>>>>>>>>>>>>>>>

    If your TS is one linking between a pair of netural reactant 
molecules and two radicals and if it can be located with UHF-MP2 
then I presume it is a diradicaloid structure. If the spin-contamination 
of the UHF solution of the diradical is moderately higher than zero (  > 0.5) 
I will be surprised you can't locate the TS with DFT. Try using 
BHandHLYP starting from your UMP2 TS structure. Use a combination of 
guess=mix and stable=opt to obtain a spin-contaminated UDFT solution
and restart the transition state search. This DFT functional has a larger mix
of Hartree-Fock exchange and should stand a better chance of 
sucess than B3LYP.


  To run CASSCF you may start from the UHF solution from the UMP2 
results. Run a pop=naturalorbitals job to get the unrestricted
orbital occupancy. Then run a UNO-CASSCF job (keyword: cas(uno,n,m)) 
with guess=read specified to read off the natural orbitals from the 
checkpoint file.  For selection of the CASSCF active space 
pick the orbitals with occupancy in the range of 0.02--1.98.

  CASSCF optimization is a real pain. I will only use it as a last resort. 

Wai-To Chan


From owner-chemistry@ccl.net Tue Nov  8 18:13:00 2005
From: "utpal;;cts.iitkgp.ernet.in" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL:G: Ab initio calculations in presence of an electric field
Message-Id: <-29907-051108143422-20575-Dnz12I81SPgCT0Ucq1T6JQ%server.ccl.net>
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Date: Wed,  9 Nov 2005 00:31:26 +051800


Sent to CCL by: [utpal|-|cts.iitkgp.ernet.in]
yes to optimize in presence of electric field you have to use field keyword in the route section. say you are applying  field,say 0.001 au, along x direction you have to write "Field=X+10" in the route
 

Kiruba Sebastina Vaji772002 . Yahoo.co.in <owner-chemistry(a)ccl.net> wrote :

> Sent to CCL by: kiruba sebastina [vaji772002 ~~ yahoo.co.in]
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> 
> Hi,
>  
> Is it possible to perform ab initio calculations in the presence of an electric
> field using the Gaussian program? If yes, could you please elaborate it.
>  
> Thank You!
>  
> Regards,
> Kiruba.
> 
> 
> 		
> ---------------------------------
>  Enjoy this Diwali with Y! India Click here
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> 
> 
> Hi,
> &nbsp;
> Is it possible to perform ab initio
> calculations in the presence of an electric field using the Gaussian program? If
> yes, could you please elaborate it.
> &nbsp;
> Thank You!
> &nbsp;
> Regards,
> Kiruba.
> 		 
> Enjoy this Diwali with Y! India http://in.promos.yahoo.com/fabmall/index.html"Click
> here
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