From owner-chemistry@ccl.net Tue Dec 1 06:08:01 2009 From: "Andrew Voronkov drugdesign[A]yandex.ru" To: CCL Subject: CCL: software for conformational analysis for the small ligands Message-Id: <-40815-091129164212-20324-zgReJO73BQzQgQHuCWFWkQ**server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 30 Nov 2009 00:08:57 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru] Dear CCL users, I am looking for software by which it's possible to analyse datasets of conformations for small molecule comounds and select most probable conformations. The academic free licenses or free licenses soft is of main interest. Best regards, Andreew From owner-chemistry@ccl.net Tue Dec 1 06:42:01 2009 From: "Andrey E Voronkov drugdesign##yandex.ru" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40816-091201061010-22084-629wAeH+bBf9VN3zQ3siSQ||server.ccl.net> X-Original-From: "Andrey E Voronkov" Date: Tue, 1 Dec 2009 06:10:07 -0500 Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru] Dear CCL users, wouldn't you be so kind to recommend the software for 3D to 2D conversion for chemical databases. The problem is that I have the results of virtuial screening in 3D SDF format which I want todisplay as planar, just visualize as organic molecule structures datasets. Are there any viewers which uatomatically covert 3D to 2D? Best regards, Andrew From owner-chemistry@ccl.net Tue Dec 1 07:59:00 2009 From: "Giuseppe Ermondi giuseppe.ermondi . unito.it" To: CCL Subject: CCL: Web servers for computer chemistry Message-Id: <-40817-091201075722-16517-8HnALMx1b9pubuSC/3FIbw,,server.ccl.net> X-Original-From: "Giuseppe Ermondi" Date: Tue, 1 Dec 2009 07:57:18 -0500 Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it] Dear CCL subscribers, I want to prepare some lessons about the use of the Web in molecular modeling and I am looking for web servers able to perform molecular mechanics and dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to introduce molecular modeling thus it will be interesting educatonal web resources, too. Does anyone know web site with this features? Thanks in advance to all! Best regards, Giuseppe From owner-chemistry@ccl.net Tue Dec 1 08:33:01 2009 From: "Michel Petitjean petitjean.chiral_+_gmail.com" To: CCL Subject: CCL: software for conformational analysis for the small ligands Message-Id: <-40818-091201080118-17592-qnFGuHQYivgPpzzCA9hPVQ.:.server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 1 Dec 2009 14:01:06 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral+/-gmail.com] Please have a look to the freeware DIVCF at itoweb.petitjean.freeware.html#DIVCF It selects a computed number of conformers among an excess of generated conformers, but without taking care about their energies: it is based on a clustering procedure. Nevertheless, I hope it helps Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean|-|cea.fr, petitjean.chiral|-|gmail.com (preferred) http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru] Dear CCL users, I am looking for software by which it's possible to analyse datasets of conformations for small molecule comounds and select most probable conformations. The academic free licenses or free licenses soft is of main interest. Best regards, Andreew From owner-chemistry@ccl.net Tue Dec 1 09:08:00 2009 From: "Meera Suri meera|*|seascapelearning.com" To: CCL Subject: CCL: Symposium on Shape/Electrostatics in India Message-Id: <-40819-091201003019-13707-XhWfgZGmbWKvyOrJiHYGhw() server.ccl.net> X-Original-From: "Meera Suri" Date: Tue, 1 Dec 2009 00:30:14 -0500 Sent to CCL by: "Meera Suri" [meera=seascapelearning.com] Seascape Learning, in collaboration with OpenEye Scientific, and Indian Scientific Experts from (JNU-New Delhi and , GVKBio-Hyderabad) is pleased to offer an Interactive Symposium on Shape and Electrostatics Best Practices for Virtual Screening and Lead-Hopping in Drug Discovery Research. The dates and locations of the symposium are as follows: JNU-New Delhi 28 and 29 Jan 2010 GVKBio Hyderabad: 3 & 4 Feb 2010 For details, including registration, please visit www.seascapelearning.com/oe_symp Seascape Learning This is a Seascape educational initiative with all proceeds going to support education in India. From owner-chemistry@ccl.net Tue Dec 1 09:43:01 2009 From: "aa aa^chemaxon.hu" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40820-091201074628-15666-rXdqdtMnKkLZzJg9IdbP4A-x-server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------010601030905090500090602" Date: Tue, 01 Dec 2009 13:46:13 +0100 MIME-Version: 1.0 Sent to CCL by: aa [aa(-)chemaxon.hu] This is a multi-part message in MIME format. --------------010601030905090500090602 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit HI Andrew, We have a couple of products for this. Either batch convert through the Marvin/MolConvert toolkit or through the Instant JChem GUI. Instant JChem personal and Marvin is free for anyone's desktop and all tools are free for academic researchers/teachers. Molconverter details and download is here:http://www.chemaxon.com/product/molcon.html and Academic Package details and sign-up is here: http://www.chemaxon.com/acpack_conditions.html . Cheers/Alex *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce Andrey E Voronkov drugdesign##yandex.ru wrote: > Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru] > Dear CCL users, > wouldn't you be so kind to recommend the software for 3D to 2D conversion for > chemical databases. The problem is that I have the results of virtuial > screening in 3D SDF format which I want todisplay as planar, just visualize as > organic molecule structures datasets. Are there any viewers which uatomatically > covert 3D to 2D? > > Best regards, > Andrew> > > --------------010601030905090500090602 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI Andrew,

We have a couple of products for this. Either batch convert through the Marvin/MolConvert toolkit or through the Instant JChem GUI. Instant JChem personal and Marvin is free for anyone's desktop and all tools are free for academic researchers/teachers.

Molconverter details and download is here:http://www.chemaxon.com/product/molcon.html and Academic Package details and sign-up is here: http://www.chemaxon.com/acpack_conditions.html .

Cheers/Alex

Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce

Andrey E Voronkov drugdesign##yandex.ru wrote: 
Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru]
Dear CCL users, 
wouldn't you be so kind to recommend the software for 3D to 2D conversion for 
chemical databases. The problem is that I have the results of virtuial 
screening in 3D SDF format which I want todisplay as planar, just visualize as 
organic molecule structures datasets. Are there any viewers which uatomatically 
covert 3D to 2D?

Best regards,
AndrewE-mail to subscribers: CHEMISTRY(-)ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST(-)ccl.net or use
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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
--------------010601030905090500090602-- From owner-chemistry@ccl.net Tue Dec 1 10:19:01 2009 From: "Wolf-D. Ihlenfeldt wdi|,|xemistry.com" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40821-091201073038-8386-jHTzCSFHZ8ys4bEkCZBC+g(a)server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 1 Dec 2009 12:58:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi*_*xemistry.com] I suggest you use the Cactvs toolkit (www.xemistry.com), free downloads = for academic users (but not for commercial applications).=20 It includes a 2D structure set viewer (csbr) which does perform 3D-2D conversion with nice atom layout on the fly from many formats, including = 3D sdf, pdb and mol2.=20 It can also export structures in 2D. For batch conversion, it is straightforward to write a custom script with the generic interpreter = (the actual core product, the viewer is just a demo application). It is = possible to configure many advanced features, such as common core orientations in = the layout, etc. Xemistry also licenses a pre-built turnkey batch converter with this features to commercial customers. W. D. Ihlenfeldt Xemistry GmbH wdi{:}xemistry.com Phone: +49 6174 201455 / Fax +49 6174 209665 --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719=20 > -----Original Message----- > From: owner-chemistry+wdi=3D=3Dxemistry.com{:}ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com{:}ccl.net] On Behalf Of Andrey E = Voronkov > drugdesign##yandex.ru > Sent: Tuesday, December 01, 2009 12:10 PM > To: Ihlenfeldt, Wolf D > Subject: CCL: 3D to 2D conversion >=20 >=20 > Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru] > Dear CCL users, > wouldn't you be so kind to recommend the software for 3D to 2D > conversion for > chemical databases. The problem is that I have the results of virtuial > screening in 3D SDF format which I want todisplay as planar, just > visualize as > organic molecule structures datasets. Are there any viewers which > uatomatically > covert 3D to 2D? >=20 > Best regards, > Andrew >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20 From owner-chemistry@ccl.net Tue Dec 1 10:54:00 2009 From: "Radu Adrian Popescu adrian_radu_popescu(!)yahoo.com" To: CCL Subject: CCL:G: solvent in gaussian Message-Id: <-40822-091130114536-23489-Oxw5q+gKHMRQAr74wEUh2g---server.ccl.net> X-Original-From: Radu Adrian Popescu Content-Type: multipart/alternative; boundary="0-116996580-1259595923=:58323" Date: Mon, 30 Nov 2009 07:45:23 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Radu Adrian Popescu [adrian_radu_popescu{=}yahoo.com] --0-116996580-1259595923=:58323 Content-Type: text/plain; charset=us-ascii Dear CCl users, Does anyone knows if I can use 1,2-dimethoxyethane as solvent for a PCM calculation in gaussian? Thank you all, Radu --0-116996580-1259595923=:58323 Content-Type: text/html; charset=us-ascii
Dear CCl users,

Does anyone knows if I can use 1,2-dimethoxyethane as solvent for a PCM calculation in gaussian?


Thank you all,

Radu


--0-116996580-1259595923=:58323-- From owner-chemistry@ccl.net Tue Dec 1 11:31:01 2009 From: "Alex Allardyce aa a chemaxon.com" To: CCL Subject: CCL: software for conformational analysis for the small ligands Message-Id: <-40823-091201075315-16167-i39Kd5k4sDCNONcpxKeGKg{:}server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------060203030407010505070202" Date: Tue, 01 Dec 2009 13:53:00 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa()chemaxon.com] This is a multi-part message in MIME format. --------------060203030407010505070202 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit HI Andrew, Not sure if this is what your looking for but our conformer generator will produce a single lowest energy conformer from an input structure in a single pass, you can try out online, or also run in batch through Marvin or Instant JChem (latest version only). All tools are free for academic researchers/teachers. Molconverter details and download is here: http://www.chemaxon.com/product/molcon.html and Academic Package details and sign-up is here: http://www.chemaxon.com/acpack_conditions.html . We released a poster on this a while back covering the approach, you can find here, http://www.chemaxon.com/conf/3D_structure_prediction_and_conformational_analysis.pdf. User feedback is good. Cheers Alex Andrew Voronkov drugdesign[A]yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru] > > Dear CCL users, > I am looking for software by which it's possible to analyse datasets of conformations for small molecule comounds and select most probable conformations. The academic free licenses or free licenses soft is of main interest. > > > Best regards, > Andreew> > > -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce --------------060203030407010505070202 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI Andrew,

Not sure if this is what your looking for but our conformer generator will produce a single lowest energy conformer from an input structure in a single pass, you can try out online, or also run in batch through Marvin or Instant JChem (latest version only).

All tools are free for academic researchers/teachers. Molconverter details and download is here: http://www.chemaxon.com/product/molcon.html and Academic Package details and sign-up is here: http://www.chemaxon.com/acpack_conditions.html .

We released a poster on this a while back covering the approach, you can find here, http://www.chemaxon.com/conf/3D_structure_prediction_and_conformational_analysis.pdf. User feedback is good.

Cheers
Alex

Andrew Voronkov drugdesign[A]yandex.ru wrote: 
Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru]

Dear CCL users,
I am looking for software by which it's possible to analyse datasets of conformations for small molecule comounds and select most probable conformations. The academic free licenses or free licenses soft is of main interest.


Best regards,
AndreewE-mail to subscribers: CHEMISTRY|-|ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST|-|ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
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Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce
--------------060203030407010505070202-- From owner-chemistry@ccl.net Tue Dec 1 12:04:01 2009 From: "andras.borosy^-^givaudan.com" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40824-091201081721-26209-MER7+ERLzZINH5Lwsbh+gA###server.ccl.net> X-Original-From: andras.borosy~~givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0045F674C125767F_=" Date: Tue, 1 Dec 2009 13:44:11 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy---givaudan.com This is a multipart message in MIME format. --=_alternative 0045F674C125767F_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mr. Voronkov, I think MOE is very good for this purpose. Best regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Andrey E Voronkov drugdesign##yandex.ru" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com\a/ccl.net 01.12.2009 12:10 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: 3D to 2D conversion Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru] Dear CCL users,=20 wouldn't you be so kind to recommend the software for 3D to 2D conversion=20 for=20 chemical databases. The problem is that I have the results of virtuial=20 screening in 3D SDF format which I want todisplay as planar, just=20 visualize as=20 organic molecule structures datasets. Are there any viewers which=20 uatomatically=20 covert 3D to 2D? Best regards, Andrew -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 0045F674C125767F_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Mr. Voronkov,

I think MOE is very good for this pu= rpose.

Best regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com


"Andrey E Voronk= ov drugdesign##yandex.ru" <owner-chemistry\a/ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com\a/ccl.net

01.12.2009 12:10
Please respond to
"CCL Subscribers" <chemistry\a/ccl.net>
To
"Borosy, Andras " <andras.borosy\a/givaudan.com>
cc
Subject
CCL: 3D to 2D conversion





Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru]
Dear CCL users,
wouldn't you be so kind to recommend the software for 3D to 2D conversion for
chemical databases. The problem is that I have the results of virtuial
screening in 3D SDF format which I want todisplay as planar, just visualize as
organic molecule structures datasets. Are there any viewers which uatomatic= ally
covert 3D to 2D?

Best regards,
Andrew



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
     http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
     http://www.ccl.net/chemistry/sub=5Funsub.shtml
     http://www.ccl.net/spammers.txt
--=_alternative 0045F674C125767F_=-- From owner-chemistry@ccl.net Tue Dec 1 12:39:01 2009 From: "Sanghwa Han hansh^^^kangwon.ac.kr" To: CCL Subject: CCL: Reversed energies by HF and B3LYP Message-Id: <-40825-091201013920-22111-0jtokRp/jbtQJvYadJjo0Q^^^server.ccl.net> X-Original-From: "Sanghwa Han" Date: Tue, 1 Dec 2009 01:39:15 -0500 Sent to CCL by: "Sanghwa Han" [hansh.:.kangwon.ac.kr] Dear Collegues, I am trying to obtain energies of anionic phenyl sulfate [C6H5-OSO3(-1)]conformers with the dihedral CC-OS of 0 and 90 degrees. When the conformers were optimized by HF/6-31G*, the 0 degree conformer had a higher (by 0.883 kJ/mol) energy than the 90 degree conformer. But single point energy calculations using B3LYP/6-31G* on the optimized structures showed that the 90 degree conformer had a higher (by 5.962 kJ/mol)energy than the 0 degree conformer. The energies were reversed with a big difference in magnitude. I tried other basis sets but always had reversed energies for B3LYP. The 90 degree conformer appears to have a lower steric energy by a visual inspection. Any comments on the matter would be appreciated. From owner-chemistry@ccl.net Tue Dec 1 13:13:00 2009 From: "Mikko Vainio mikko.vainio() abo.fi" To: CCL Subject: CCL: software for conformational analysis for the small ligands Message-Id: <-40826-091201082533-29909-ba9XX8qOLg4KvgDYv6LqJw!A!server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 01 Dec 2009 14:54:12 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio,,abo.fi] Andrew Voronkov drugdesign[A]yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru] > > Dear CCL users, > I am looking for software by which it's possible to analyse datasets of conformations for small molecule comounds and select most probable conformations. The academic free licenses or free licenses soft is of main interest. > > > Best regards, > Andreew > Hi Andreew, Balloon (http://users.abo.fi/mivainio/balloon/) generates conformer ensembles for small molecules. It is free to use for any purpose except selling the program itself. Regards, Mikko From owner-chemistry@ccl.net Tue Dec 1 13:48:01 2009 From: "Michel Petitjean petitjean.chiral[a]gmail.com" To: CCL Subject: CCL: software for conformational analysis for the small ligands Message-Id: <-40827-091201093321-24574-GLzXE0Aoz8hlPQiirrXZkA(!)server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 1 Dec 2009 15:33:08 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral(~)gmail.com] Sorry, I didn't specify the full URL: it is http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#DIVCF Sent to CCL by: Michel Petitjean [petitjean.chiral+/-gmail.com] Please have a look to the freeware DIVCF at itoweb.petitjean.freeware.html#DIVCF It selects a computed number of conformers among an excess of generated conformers, but without taking care about their energies: it is based on a clustering procedure. Nevertheless, I hope it helps Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean_-_cea.fr, petitjean.chiral_-_gmail.com (preferred) http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru] Dear CCL users, I am looking for software by which it's possible to analyse datasets of conformations for small molecule comounds and select most probable conformations. The academic free licenses or free licenses soft is of main interest. Best regards, Andreew From owner-chemistry@ccl.net Tue Dec 1 14:27:00 2009 From: "Carlos F. Lagos carlos\a/cbuc.cl" To: CCL Subject: CCL: Web servers for computer chemistry Message-Id: <-40828-091201095310-9195-vj/eRwjKxq4DW6CL7oabVw^server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 1 Dec 2009 11:46:47 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos^^^cbuc.cl] For chemometrics calculations and further analysis you might consider the Virtual Computational Chemistry Laboratory server (http://www.vcclab.org/). QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo I 8330025 Santiago-Chile Phone: +56 2 3541911 I http://www.cbuc.cl -----Mensaje original----- De: owner-chemistry+carlos==cbuc.cl/a\ccl.net [mailto:owner-chemistry+carlos==cbuc.cl/a\ccl.net] En nombre de Giuseppe Ermondi giuseppe.ermondi . unito.it Enviado el: Martes, 01 de Diciembre de 2009 09:57 Para: Lagos, Carlos F Asunto: CCL: Web servers for computer chemistry Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it] Dear CCL subscribers, I want to prepare some lessons about the use of the Web in molecular modeling and I am looking for web servers able to perform molecular mechanics and dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to introduce molecular modeling thus it will be interesting educatonal web resources, too. Does anyone know web site with this features? Thanks in advance to all! Best regards, Giuseppehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________ Information from ESET NOD32 Antivirus, version of virus signature database 4651 (20091201) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __________ Information from ESET NOD32 Antivirus, version of virus signature database 4651 (20091201) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com From owner-chemistry@ccl.net Tue Dec 1 14:58:00 2009 From: "Dr. M. F. Somers m.somers{=}chem.leidenuniv.nl" To: CCL Subject: CCL: Web servers for computer chemistry Message-Id: <-40829-091201101820-30066-cpVtY1nfkdK+w2bJutoBqw_-_server.ccl.net> X-Original-From: "Dr. M. F. Somers" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Tue, 1 Dec 2009 15:40:40 +0100 MIME-Version: 1.0 Sent to CCL by: "Dr. M. F. Somers" [m.somers{}chem.leidenuniv.nl] Hi, You might want to take a look at http://boinc.gorlaeus.net m. On Tuesday 01 December 2009 13:57, Giuseppe Ermondi giuseppe.ermondi .=20 unito.it wrote: > Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it] > Dear CCL subscribers, > > I want to prepare some lessons about the use of the Web in molecular > modeling and I am looking for web servers able to perform molecular > mechanics and dynamic calculations and chemometrics analysis (PLS, PCA). > The goal is to introduce molecular modeling thus it will be interesting > educatonal web resources, too. Does anyone know web site with this > features? > > Thanks in advance to all! > > Best regards, > > Giuseppe > > =2D-=20 Dr. M. F. Somers Theoretical Chemistry - Leiden Institute of Chemistry =C2=A0- Leiden Univer= sity Einsteinweg 55, P.B. 9502, 2300 RA Leiden, The Netherlands tel: +31715274437 mail: m.somers=-=chem.leidenuniv.nl web: =C2=A0http://theorchem.leidenuniv.nl/en/people/somers room: Gorlaeus Labs, Einsteinweg 55, 2333 CC, Leiden, HB322. From owner-chemistry@ccl.net Tue Dec 1 15:33:01 2009 From: "ros rodrigogalindo~~gmail.com" To: CCL Subject: CCL: Web servers for computer chemistry Message-Id: <-40830-091201122314-19761-tceN9kqW1nU1oSzAMbU9sA*server.ccl.net> X-Original-From: ros Content-Type: multipart/alternative; boundary=0015177409889014b70479ae0226 Date: Tue, 1 Dec 2009 11:23:01 -0600 MIME-Version: 1.0 Sent to CCL by: ros [rodrigogalindo*_*gmail.com] --0015177409889014b70479ae0226 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You can try http://www.dockingserver.com/web They allow 2 free docking calculations a day and you can draw the input molecules directly in their website. Hope it helps. Rodrigo. ----------------------------- Instituto de Qu=EDmica Universidad Nacional Aut=F3noma de M=E9xico 2009/12/1 Giuseppe Ermondi giuseppe.ermondi . unito.it < owner-chemistry*ccl.net> > > Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it] > Dear CCL subscribers, > > I want to prepare some lessons about the use of the Web in molecular > modeling > and I am looking for web servers able to perform molecular mechanics and > dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to > introduce molecular modeling thus it will be interesting educatonal web > resources, too. Does anyone know web site with this features? > > Thanks in advance to all! > > Best regards, > > Giuseppe > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --0015177409889014b70479ae0226 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You can try

http://www.= dockingserver.com/web

They allow 2 free docking calculations a d= ay and you can draw the input molecules directly in their website.

Hope it helps.


Rodrigo.
-----------------------------
Inst= ituto de Qu=EDmica
Universidad Nacional Aut=F3noma de M=E9xico

2009/12/1 Giuseppe Ermondi giuseppe.ermondi . unito.it <owner-chemistry*ccl.net>

Sent to CCL by: "Giuseppe =A0Ermondi" [giuseppe.ermondi*_*unito.it]
Dear CCL subscribers,

I want to prepare some lessons about =A0the use of the Web in molecular mod= eling
and I am looking for web servers able to perform molecular mechanics and dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to introduce molecular modeling thus it will be interesting educatonal web
resources, too. Does anyone know web site with this features?

Thanks in advance to all!

Best regards,

Giuseppe



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--0015177409889014b70479ae0226-- From owner-chemistry@ccl.net Tue Dec 1 16:08:00 2009 From: "Prakash Rathi prakashrathi(~)hotmail.com" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40831-091201101435-26308-7W38XYwnDiOJaDtfvz063w_+_server.ccl.net> X-Original-From: "Prakash Rathi" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00DA_01CA72C2.739559B0" Date: Tue, 1 Dec 2009 20:11:21 +0530 MIME-Version: 1.0 Sent to CCL by: "Prakash Rathi" [prakashrathi%a%hotmail.com] This is a multi-part message in MIME format. ------=_NextPart_000_00DA_01CA72C2.739559B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Andrew, The one best software to convert 3D sdf structures to 2D is MOE. It has = option to convert 3D to 2D alongwith the options for retaining Hydrogens = or omitting the Hydrogen in 2D structure. __________________________________________________________ Regards- Prakash Chandra Rathi Research Fellow, Department of Medicinal Chemistry, Block- A (Room No.- 208), National Institute of Pharmaceutical Education & Research (NIPER) Sec- 67, S.A.S. Nagar-160062, Punjab (India) Institute website: www.niper.gov.in Ph. 09357399021 __________________________________________________________ ------=_NextPart_000_00DA_01CA72C2.739559B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Andrew,
The one best software to convert 3D sdf = structures=20 to 2D is MOE. It has option to convert 3D to 2D alongwith the options = for=20 retaining Hydrogens or omitting the Hydrogen in 2D = structure.
__________________________________________________________Regards-
Prakash=20 Chandra Rathi
Research Fellow, Department of Medicinal = Chemistry,
Block- A=20 (Room No.- 208),
National Institute of Pharmaceutical Education & = Research (NIPER)
Sec- 67, S.A.S. Nagar-160062, Punjab = (India)
Institute=20 website: www.niper.gov.in
Ph. = 09357399021
__________________________________________________________=
------=_NextPart_000_00DA_01CA72C2.739559B0-- From owner-chemistry@ccl.net Tue Dec 1 16:44:00 2009 From: "javier sacristan sacristan.javier+*+gmail.com" To: CCL Subject: CCL: calculating charges in MD simulation, best approach? Message-Id: <-40832-091201104156-19534-ss4HRvi6ACHBg0j/5ZBJtw .. server.ccl.net> X-Original-From: "javier sacristan" Date: Tue, 1 Dec 2009 10:41:53 -0500 Sent to CCL by: "javier sacristan" [sacristan.javier%%gmail.com] Hi CCLrs I am interested in building some polymers from some small compounds (not simply monomers). So what do you think that would be the best approach in order to set up the charges of each atom in these compounds before running a MD simulation. a)qeq b)Gasteiger c)charges from the forcefield thanks for reading From owner-chemistry@ccl.net Tue Dec 1 17:22:00 2009 From: "Joe Corkery jcorkery-#-eyesopen.com" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40833-091201113621-28396-jnlS4A+kGAABFwyLtFuLwg/a\server.ccl.net> X-Original-From: Joe Corkery Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 1 Dec 2009 08:35:35 -0800 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery++eyesopen.com] Dear Andrey, OpenEye provides a couple of options which might be of interest to you. VID= A (http://www.eyesopen.com/products/applications/vida-vivant.html) is our v= isualizer which is capable of loading and browsing through large databases = of molecules. You can view the molecules in 2D, 3D or both simultaneously a= s desired. It also includes a built-in chemically aware spreadsheet which c= an be particularly useful when looking at virtual screening results. However, if you are looking to convert the database wholesale to 2D coordin= ates or directly to 2D images, the Ogham TK (http://www.eyesopen.com/produc= ts/toolkits/cheminformatics-toolkits.html) can provide that functionality. OpenEye software is free for non-commercial use. You can apply for a academ= ic/non-commercial license at the following location: http://www.eyesopen.com/forms/academic_license_app.php Sincerely, Joe Corkery OpenEye Scientific Software www.eyesopen.com -----Original Message----- > From: owner-chemistry+jcorkery=3D=3Deyesopen.com|a|ccl.net [mailto:owner-chem= istry+jcorkery=3D=3Deyesopen.com|a|ccl.net] On Behalf Of Andrey E Voronkov dr= ugdesign##yandex.ru Sent: Tuesday, December 01, 2009 6:10 AM To: Joe Corkery Subject: CCL: 3D to 2D conversion Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru] Dear CCL users,=20 wouldn't you be so kind to recommend the software for 3D to 2D conversion f= or=20 chemical databases. The problem is that I have the results of virtuial=20 screening in 3D SDF format which I want todisplay as planar, just visualize= as=20 organic molecule structures datasets. Are there any viewers which uatomatic= ally=20 covert 3D to 2D? Best regards, Andrew -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Dec 1 17:53:00 2009 From: "Radoslaw Kaminski rkaminski.rk,gmail.com" To: CCL Subject: CCL: Reversed energies by HF and B3LYP Message-Id: <-40834-091201151807-16342-WA20riSxXTvA9mMA+VdWsw[*]server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=00504502cd47add4e40479af9c2e Date: Tue, 1 Dec 2009 14:17:41 -0500 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk^gmail.com] --00504502cd47add4e40479af9c2e Content-Type: text/plain; charset=ISO-8859-1 Hi, It could be difference in methods themselfs. DFT takes more factors into account than HF but that is not always the best thing (!). I could suggest to do DFT calculations with some big basis set like aug-cc-PVDZ for B3LYP, BP86 functionals. Also you could set up some calculations with MP2 method, also with big basis set. I could mainly trust such results so you could have some reference point for comparison. The point is what are you going to analyse anyway? If you want to do quantitavie analysis I would go to MP2 with big basis sets and compare them with DFT results. From my experiemce even if you use B3LYP with 6-311++G** basis set it gives sometimes totally different results (lack of one minium of energy!) compared to B3LYP/aug-cc-pVDZ which was more or less the same as in MP2 calculation. Hope it helps, Radek 2009/12/1 Sanghwa Han hansh^^^kangwon.ac.kr > > Sent to CCL by: "Sanghwa Han" [hansh.:.kangwon.ac.kr] > Dear Collegues, > > I am trying to obtain energies of anionic phenyl sulfate > [C6H5-OSO3(-1)]conformers with the dihedral CC-OS of 0 and 90 degrees. > When the conformers were optimized by HF/6-31G*, the 0 degree conformer had > a higher (by 0.883 kJ/mol) energy than the 90 degree conformer. > But single point energy calculations using B3LYP/6-31G* on the optimized > structures showed that the 90 degree conformer had a higher (by 5.962 > kJ/mol)energy than the 0 degree conformer. The energies were reversed with a > big difference in magnitude. > I tried other basis sets but always had reversed energies for B3LYP. > The 90 degree conformer appears to have a lower steric energy by a visual > inspection. > > Any comments on the matter would be appreciated.> > > --00504502cd47add4e40479af9c2e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

It could be difference in methods themselfs. DFT takes more fact= ors into account than HF but that is not always the best thing (!). I could= suggest to do DFT calculations with some big basis set like aug-cc-PVDZ fo= r B3LYP, BP86 functionals. Also you could set up some calculations with MP2= method, also with big basis set. I could mainly trust such results so you = could have some reference point for comparison.

The point is what are you going to analyse anyway? If you want to do qu= antitavie analysis I would go to MP2 with big basis sets and compare them w= ith DFT results. From my experiemce even if you use B3LYP with 6-311++G** b= asis set it gives sometimes totally different results (lack of one minium o= f energy!) compared to B3LYP/aug-cc-pVDZ=A0 which was more or less the same= as in MP2 calculation.

Hope it helps,

Radek


2009/= 12/1 Sanghwa Han hansh^^^kangwon.ac.kr= <owner-che= mistry###ccl.net>

Sent to CCL by: "Sanghwa =A0Han" [hansh.:.kangwon.ac.kr]
Dear Collegues,

I am trying to obtain energies of anionic phenyl sulfate [C6H5-OSO3(-1)]con= formers with the dihedral CC-OS of 0 and 90 degrees.
When the conformers were optimized by HF/6-31G*, the 0 degree conformer had= a higher (by 0.883 kJ/mol) energy than the 90 degree conformer.
But single point energy calculations using B3LYP/6-31G* on the optimized st= ructures showed that the 90 degree conformer had a higher (by 5.962 kJ/mol)= energy than the 0 degree conformer. The energies were reversed with a big d= ifference in magnitude.
I tried other basis sets but always had reversed energies for B3LYP.
The 90 degree conformer appears to have a lower steric energy by a visual i= nspection.

Any comments on the matter would be appreciated.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY###ccl.n= et or use:
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--00504502cd47add4e40479af9c2e-- From owner-chemistry@ccl.net Tue Dec 1 20:52:00 2009 From: "qiancheng shen qianchengshen],[gmail.com" To: CCL Subject: CCL: Web servers for computer chemistry Message-Id: <-40835-091201205117-30705-KFqFRi/OvzRpJUdgUsMRBw+*+server.ccl.net> X-Original-From: qiancheng shen Content-Type: multipart/alternative; boundary=001636163f259675540479b51b12 Date: Wed, 2 Dec 2009 09:51:05 +0800 MIME-Version: 1.0 Sent to CCL by: qiancheng shen [qianchengshen.##.gmail.com] --001636163f259675540479b51b12 Content-Type: text/plain; charset=ISO-8859-1 You may try www.dddc.ac.cn/some and www.dddc.ac.cn/admetus. They are all about prediction for ADMET properties of small molecules. 2009/12/1 Giuseppe Ermondi giuseppe.ermondi . unito.it < owner-chemistry##ccl.net> > > Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it] > Dear CCL subscribers, > > I want to prepare some lessons about the use of the Web in molecular > modeling > and I am looking for web servers able to perform molecular mechanics and > dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to > introduce molecular modeling thus it will be interesting educatonal web > resources, too. Does anyone know web site with this features? > > Thanks in advance to all! > > Best regards, > > Giuseppe> > > --001636163f259675540479b51b12 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You may try www.dddc.ac.cn/some = and www.dddc.ac.cn/admetus. T= hey are all about prediction for ADMET properties of small molecules.
<= br>
2009/12/1 Giuseppe Ermondi giuseppe.ermondi . unito.it <owner-chemistry##ccl.net>

Sent to CCL by: "Giuseppe =A0Ermondi" [giuseppe.ermondi*_*unito.it]
Dear CCL subscribers,

I want to prepare some lessons about =A0the use of the Web in molecular mod= eling
and I am looking for web servers able to perform molecular mechanics and dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to introduce molecular modeling thus it will be interesting educatonal web
resources, too. Does anyone know web site with this features?

Thanks in advance to all!

Best regards,

Giuseppe

--001636163f259675540479b51b12-- From owner-chemistry@ccl.net Tue Dec 1 22:40:01 2009 From: "Jing Kong jkong- -q-chem.com" To: CCL Subject: CCL: Workshop on electronic structure calculations (second announcement) Message-Id: <-40836-091201184232-16074-9+sfv5yTN06Wl1lGPN1A7g],[server.ccl.net> X-Original-From: "Jing Kong" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 1 Dec 2009 18:42:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong(_)q-chem.com] Dear colleague, This is the second announcement for the Workshop on Electronic Structure Calculations at the University of California, Berkeley on December 10th and 11th. The workshop is composed of seminars, hands-on tutorials and posters. The registration deadline has been extended to December 6th. New customers will receive a free half-year group license if registered by that date. The full schedule of the workshop is now available (http://www.q-chem.com/wsca_schedule.html). Please bring your laptop for the workshop. For details and registration please visit the workshop website (http://www.q-chem.com/wsca_hh.html). The workshop is free of charge. We apologize if you have received multiple copies of this email. We look forward to seeing you at the workshop. Sincerely, Jing Kong, Ph.D. CEO & Chief Scientist Q-Chem, Inc. From owner-chemistry@ccl.net Tue Dec 1 23:15:01 2009 From: "Ye Qing yeqing^^^ihep.ac.cn" To: CCL Subject: CCL:G: Questions about the CPCM calculation Message-Id: <-40837-091201215413-29675-dWTTvNmCVsFNdr8SMR68KQ%%server.ccl.net> X-Original-From: "Ye Qing" Date: Tue, 1 Dec 2009 21:54:09 -0500 Sent to CCL by: "Ye Qing" [yeqing#,#ihep.ac.cn] Hello everyone: I am a new learner of Gaussian, recently I am doing a PES scan on an ion-water system under the solvent condition by employing the CPCM method, my goal is to obtain the so-called "effective two body ion-water potential" with an expression as follow: U(ion-water)=<|H|>(ion-water)-<|H|>(ion)-<|H|>(water); where the wave function is perturbed by the solvent effect according to the CPCM, and the Hamiltonian operators H refer to the ion-water, bare ion, and bare water molecule in a vacuum. But the final results in the Gaussian output file are only the total potential energy (including interaction energy of atoms inside water molecular). And in each scan step, there are some informations as follow: SCF Done: E(ROHF) = -122.403701658 A.U. after 5 cycles Convg = 0.1238D-04 -V/T = 2.0537 S**2 = 0.0000 KE= 1.161682886018D+02 PE=-3.457851817425D+02 EE= 8.218447783564D+01 -------------------------------------------------------------------- Variational C-PCM results ========================= (a.u.) = -121.748559 (a.u.) = -122.403702 Total free energy in solution: with all non electrostatic terms (a.u.) = -122.397421 -------------------------------------------------------------------- (Polarized solute)-Solvent (kcal/mol) = -411.11 -------------------------------------------------------------------- Cavitation energy (kcal/mol) = 6.86 Dispersion energy (kcal/mol) = -5.90 Repulsion energy (kcal/mol) = 2.98 Total non electrostatic (kcal/mol) = 3.94 -------------------------------------------------------------------- Partition over spheres: Sphere on Atom Surface Charge GEl GCav GDR 1 Cd1 31.50 -1.757 -347.61 3.44 -0.23 2 O2 31.30 0.099 -7.03 3.42 -2.69 Added spheres: 10.78 -0.329 -56.48 0.00 0.00 -------------------------------------------------------------------- After PCM corrections, the SCF energy is -122.403701658 a.u. I guess Gaussian scan job can provide the value of the first term of the U (ion-water) expression, perhaps I need to do another two single point calculation in order to obtain the second and third term of the U(ion- water) expression. But I don't know where is the value of the first term in the U(ion-water) expression (<|H|>(ion-water)) in Gaussian output file? Can anyone help me on this problem? I wil be very grateful for your help. Best Wishes! Sincerely: QingYe