From owner-chemistry@ccl.net Tue Jun 24 02:50:00 2014 From: "Mannan K malie_03###yahoo.co.in" To: CCL Subject: CCL: diversity set for virtual screening Message-Id: <-50276-140624024644-24225-bAxbLDssIDRZca5nF5VRVA!A!server.ccl.net> X-Original-From: "Mannan K" Date: Tue, 24 Jun 2014 02:46:43 -0400 Sent to CCL by: "Mannan K" [malie_03*_*yahoo.co.in] Hi CCLers, I want to do a virtual screening against a protein of my interest. To begin, I would like to start with relatively small diversity set to save some computational time. Where do I get a diverse chemical set. or Do i need to prepare a library of my own diverse set? or Is there any other way to begin? Many Thanks for your time, Mannan From owner-chemistry@ccl.net Tue Jun 24 03:24:00 2014 From: "M M mozhdehmohammadpour^-^gmail.com" To: CCL Subject: CCL: resonance Raman calculation with IMDHO method in ORCA Message-Id: <-50277-140624031555-6076-qwC6cT1GXHL44L9zY69Sig^server.ccl.net> X-Original-From: "M M" Date: Tue, 24 Jun 2014 03:15:46 -0400 Sent to CCL by: "M M" [mozhdehmohammadpour|*|gmail.com] we are interested in using IMDHO method for calculating resonance Raman which is implemented in ORCA suit of program. According to our previous results, we are so enthusiastic about finding Raman scattering factors using SAOP functional in DFT method and considering the fact that this functional is not implemented in ORCA yet, I would like to know is it possible to use electronic excitation energy and transition dipole moments which we have found from SAOP or any other functionals by changing manually some parts of prior calculations of resonance Raman (such as .hess or .rrhess files) in order to have appropriate dimensionless displacements in .asa.inp based on SAOP functional? and if yes, how? If it is possible, I would be grateful if you could tell me the procedure. I appreciate any other comment. Thanks in advance. M.M From owner-chemistry@ccl.net Tue Jun 24 03:59:00 2014 From: "Frank Neese Frank.Neese.:.cec.mpg.de" To: CCL Subject: CCL: resonance Raman calculation with IMDHO method in ORCA Message-Id: <-50278-140624035604-14270-YOGCPwcHsS9A2zCWaCs99w:server.ccl.net> X-Original-From: "Frank Neese" Date: Tue, 24 Jun 2014 03:56:02 -0400 Sent to CCL by: "Frank Neese" [Frank.Neese^cec.mpg.de] The way this works is that ORCA produces an ASCII input file for the orca_asa program which then simulates the resonance Raman spectra. In the ASA input file there are all kind of parameter including transition energies and transition moments. Wherever they come from is your responsibility as a user. They can be generated by ORCA but don't have to be. You can replace them by SAOP values if you insist on this functional (we have no plans to implement it). This is all carefully described in the manual of the ORCA program that should be consulted for these matters. Good luck! Sent to CCL by: "M M" [mozhdehmohammadpour|*|gmail.com] we are interested in using IMDHO method for calculating resonance Raman which is implemented in ORCA suit of program. According to our previous results, we are so enthusiastic about finding Raman scattering factors using SAOP functional in DFT method and considering the fact that this functional is not implemented in ORCA yet, I would like to know is it possible to use electronic excitation energy and transition dipole moments which we have found from SAOP or any other functionals by changing manually some parts of prior calculations of resonance Raman (such as .hess or .rrhess files) in order to have appropriate dimensionless displacements in .asa.inp based on SAOP functional? and if yes, how? If it is possible, I would be grateful if you could tell me the procedure. I appreciate any other comment. Thanks in advance. M.M From owner-chemistry@ccl.net Tue Jun 24 04:35:01 2014 From: "Michael Florian Peintinger mpei()thch.uni-bonn.de" To: CCL Subject: CCL: Imaginary Frequencies in Orca Message-Id: <-50279-140624040637-25468-+pru4QUvyy939xBuOOOiAQ-,-server.ccl.net> X-Original-From: Michael Florian Peintinger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Jun 2014 10:06:26 +0200 MIME-Version: 1.0 Sent to CCL by: Michael Florian Peintinger [mpei[a]thch.uni-bonn.de] Dear Christopher, there is a forum for all ORCA related questions: https://cec.mpg.de/forum/portal.php Here the ORCA developers give you direct support on the use of the program. All the best Michael Am 23.06.14 20:45, schrieb Shepard, Christopher chris.shepard*richmond.edu: > I am trying to optimize different benzene dimer cation structures on > multiple model chemistry's, but each time I use the basis set aug-cc-pVTZ I > get multiple imaginary frequencies. I've including different keywords such > as TightOpt, VeryTightSCF, Grid6, NoFinalGrid and > %scf convcheck mode 0 > maxiter 2000 > end. > but I still end up with at least 2 imaginary frequencies. Is there another > way to deal with this issue? > > Thanks in advance for the help, Chris > > I have attached a copy of my original input file and the relevant output it > gave me. > From owner-chemistry@ccl.net Tue Jun 24 07:52:00 2014 From: "K.K.Reddy kkreddy412_._gmail.com" To: CCL Subject: CCL: diversity set for virtual screening Message-Id: <-50280-140624052546-26950-HOJV7llBnpjLB91k3jRRRA(0)server.ccl.net> X-Original-From: "K.K.Reddy" Content-Type: multipart/alternative; boundary=089e0112cbfcfe6eb604fc918a62 Date: Tue, 24 Jun 2014 14:55:39 +0530 MIME-Version: 1.0 Sent to CCL by: "K.K.Reddy" [kkreddy412]![gmail.com] --089e0112cbfcfe6eb604fc918a62 Content-Type: text/plain; charset=ISO-8859-1 You can download diverset from ChemBridge and perform virtual screening. Cheers, KK Reddy -------------------------------------------------------------------------- Karnati Konda Reddy PhD student Department of Bioinformatics, Alagappa University Karaikudi-630 004, Tamil Nadu, INDIA Mobile:+91-9786082031 E-mail: kkreddy412###gmail.com Web: http://www.sanjeevslab.org ---------------------------------------------------------------------- On Tue, Jun 24, 2014 at 12:16 PM, Mannan K malie_03###yahoo.co.in < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: "Mannan K" [malie_03*_*yahoo.co.in] > Hi CCLers, > > I want to do a virtual screening against a protein of my interest. > To begin, I would like to start with relatively small diversity set to > save some computational time. > Where do I get a diverse chemical set. > or Do i need to prepare a library of my own diverse set? > or Is there any other way to begin? > > Many Thanks for your time, > > Mannan> > > --089e0112cbfcfe6eb604fc918a62 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
You can download diverset from ChemBridge and pe= rform virtual screening.

Cheers,
KK Reddy

-----------------------------= ---------------------------------------------
Karnati Konda Reddy
PhD student
Department of Bioinformatics, Alagapp= a University
Karaikudi-630 004, Tamil Nadu, INDIA
Mobile:+91-97860820= 31 E-mail: kkreddy41= 2###gmail.com
Web: http://www.sanjeevslab.o= rg
----------------------------------------------------------------------
<= br>


On Tue, Jun 24, 2014 at 12:16 PM, Mannan= K malie_03###yahoo.co.in <owner-= chemistry###ccl.net> wrote:

Sent to CCL by: "Mannan =A0K" [malie_03*_*yahoo.co.in]
Hi CCLers,

I want to do a virtual screening against a protein of my interest.
To begin, I would like to start with relatively small diversity set to save= some computational time.
Where do I get a diverse chemical set.
or Do i need to prepare a library of my own diverse set?
or Is there any other way to begin?

Many Thanks for your time,

Mannan



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--089e0112cbfcfe6eb604fc918a62-- From owner-chemistry@ccl.net Tue Jun 24 09:01:01 2014 From: "Robin Chaudret Robin.Chaudret=-=scienomics.com" To: CCL Subject: CCL:G: Scienomics Free Web Seminar Friday June 27th on "Modeling Thermodynamic Properties with PC-SAFT Equation of State Theory" Message-Id: <-50281-140624085313-25069-CIuap1p4+2HjH+sF2M3uKA/./server.ccl.net> X-Original-From: Robin Chaudret Content-Type: multipart/alternative; boundary="------------080505080601060405060907" Date: Tue, 24 Jun 2014 14:53:02 +0200 MIME-Version: 1.0 Sent to CCL by: Robin Chaudret [Robin.Chaudret%scienomics.com] This is a multi-part message in MIME format. --------------080505080601060405060907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear all, Scienomics is pleased to announce the 6^th *Materials Modeling and Simulations Seminar,* which will take place on Friday June^27th , 2014 at 17:30 Standard European Summer Time (GMT+2). This seminar is part of Scienomics' monthly web seminars which cover all aspects of Materials Science modeling and simulations with MAPS 3.4. The topic of this seminar is Modeling Thermodynamic Properties with PC-SAFT Equation of State Theory as implemented in our SciTherm and SciPharma MAPS plugins. Applications from the Chemical Industry, the Oil and Gas Industry and the Pharmaceutical Industry will be covered. Additionally one example how atomistic modeling and EOS modeling can work hand in hand will be demonstrated on the case of phase diagram prediction of a phenol-water mixture. The following cases will be presented: 1. Phase diagram of phenol-water. 2. Vapor-liquid equilibrium of the ternary system carbon dioxide-water-methanol. 3. Copolymer-solvent phase equilibrium. 4. Phase equilibrium of electrolytes. Solubility of gases in ionic liquids. 5. Solubility of pharmaceuticals in pure and mixed solvents. Comparison between a PC-SAFT based approach and NRTL-SAC. The registration form for the upcoming Scienomics web seminar can be found here . Join us ! Hope to see many of you there, Robin Chaudret -- --------------080505080601060405060907 Content-Type: multipart/related; boundary="------------030308040108090401010803" --------------030308040108090401010803 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

Dear all,

Scienomics is pleased to announce the 6th Materials Modeling and Simulations Seminar, which will take place on Friday June27th, 2014 at 17:30 Standard European Summer Time (GMT+2).

This seminar is part of Scienomics' monthly web seminars which cover all aspects of Materials Science modeling and simulations with MAPS 3.4.

The topic of this seminar is Modeling Thermodynamic Properties with PC-SAFT Equation of State Theory as implemented in our SciTherm and SciPharma MAPS plugins.

Applications from the Chemical Industry, the Oil and Gas Industry and the Pharmaceutical Industry will be covered. Additionally one example how atomistic modeling and EOS modeling can work hand in hand will be demonstrated on the case of  phase diagram prediction of a phenol-water mixture. The following cases will be presented:

1.  Phase diagram of phenol-water.

2.  Vapor-liquid equilibrium of the ternary system carbon dioxide-water-methanol.

3.  Copolymer-solvent phase equilibrium.

4.  Phase equilibrium of electrolytes. Solubility of gases in ionic liquids.

5.  Solubility of pharmaceuticals in pure and mixed solvents. Comparison between a PC-SAFT based approach and NRTL-SAC.

The registration form for the upcoming Scienomics web seminar can be found here. Join us !

Hope to see many of you there,

Robin Chaudret

--
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ZlbDAMwtmjBY5JIypJANdT4fgvrXSjBqDSNMl1ciMySeYxh85/Ky2ST+72dTn15zQBr0UUUA FFFFABRRRQAUUUUAFFFFABRRRQAUUUUAFFFFABRRRQAUUUUAFFFFABRRRQAUUUUAFFFFABRR RQAUUUUAFFFFABRRRQAUUUUAFFFFABRRRQAUUUUAFFFFABRRRQAUUUUAFFFFABRRRQAUUUUA f//Z --------------030308040108090401010803-- --------------080505080601060405060907-- From owner-chemistry@ccl.net Tue Jun 24 14:53:00 2014 From: "Chelsea Mueller cmueller1893,,gmail.com" To: CCL Subject: CCL:G: "Atomic number out of range in MkApno" in Gaussian 09 Message-Id: <-50282-140624122554-768-kK+KbebOfH6BAucR4QS4EQ^_^server.ccl.net> X-Original-From: "Chelsea Mueller" Date: Tue, 24 Jun 2014 12:25:53 -0400 Sent to CCL by: "Chelsea Mueller" [cmueller1893(~)gmail.com] Hello, I am working on a Gaussian 09 QST3 calculation involving several iron carbonyl complexes. The calculation fails with the error: Atomic number out of range in MkApno. Here is the command line I am using and the basis set information: #p opt=(QST3,CARTESIAN) pop=full b3lyp gen IOP(3/33=1) scf=tight gfinput scfcyc=150 pseudo-read C H O 0 6-31G(d) **** Fe 0 SDD **** Any insight would be appreciated. Thank you, Chelsea