From owner-chemistry@ccl.net Mon Apr 7 00:47:00 2008 From: "Arvydas Tamulis tamulis]=[mserv.itpa.lt" To: CCL Subject: CCL:G: Where might be my mistake in calculation by Turbomole using TDDFT? Message-Id: <-36654-080407004416-25068-3Bnb3hT/gN+1MDQz5EXzkg|-|server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 7 Apr 2008 07:43:53 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis!=!mserv.itpa.lt] Dear Mariusz, Thank you for your lesson. I am new in Turbomole. We have done solely specification of solvent but received very bad Turbomole TDDFT B3LYP/LanL2DZ spectrum of [Ru(bpy)3]2+ in comparison with right spectrum obtained by Gaussian03: Excited State 5: Singlet-E 2.7424 eV 452.09 nm f=0.0077 Excited State 6: Singlet-E 2.7424 eV 452.09 nm f=0.0077 Excited state symmetry could not be determined. Excited State 7: Singlet-?Sym 2.8873 eV 429.41 nm f=0.1097 Excited state symmetry could not be determined. Excited State 8: Singlet-?Sym 2.8873 eV 429.41 nm f=0.1097 (f - are bad in G03 for [Ru(bpy)3]2+) Where might be my mistake in calculation by Turbomole using TDDFT B3LYP spectrum of [Ru(bpy)3]2+ using COSMO ? By the way, I did not found the LanL2DZ basis set in Turbomole. Which basis set is good for Ru atom in Turbomole?? With best regards, Arvydas Tamulis On Sun, 6 Apr 2008, Mariusz Radon mariusz.radon-x-gmail.com wrote: > > Sent to CCL by: Mariusz Radon [mariusz.radon()gmail.com] > Dear Arvydas, > > What do you mean by ``solvent atoms''? >> I can't find a way to specify a solvent (methanol) atoms. > > http://www.turbomole-gmbh.com/manuals/version_5_9/DOK_HTML/node253.html#21382 > > AFAIK, in COSMO you specify the solvent _solely_ by its dielectric > permitivity (epsilon) and ``effective radius'' (rsolv), and several less > important parameters to control cavity construction. > > regards, > Mariusz Radon > > -- > Mariusz Radon > Department of Theoretical Chemistry > Jagiellonian University > mradon /at/ chemia.uj.edu.pl > http://www.chemia.uj.edu.pl/~mradon> > From owner-chemistry@ccl.net Mon Apr 7 02:51:01 2008 From: "Pablo Vitoria pablo.vitoria . ehu.es" To: CCL Subject: CCL: opening linux (64-bit) genereated .chk files on PC (revisited) Message-Id: <-36655-080407025001-20687-Qy34UurLqywvJgettWgPGg#%#server.ccl.net> X-Original-From: Pablo Vitoria Content-Type: multipart/mixed; boundary="------------020603040903070702050701" Date: Mon, 07 Apr 2008 08:49:40 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria [pablo.vitoria_+_ehu.es] This is a multi-part message in MIME format. --------------020603040903070702050701 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Soren, The .chk file is a binary file, and you should not try to convert it with dos2unix (or todos) since these are programs designed to be ran on text files. You'll probably get a corrupted file. You should run formchk on the .chk file in the 64-bit system computer, not in Windows. And then either open the formatted checkpoint file (.fchk), or back-transform it to .chk in Windows. Pablo Soren Eustis soren[*]jhu.edu escribió: > > I received some responses to my earlier inquiry regarding a problem I > am having visualizing and/or reading .chk files generated on a linux > 64-bit system with a windows 32-bit system. So far, the problem > remains, and I am hoping someone else may have some ideas. > > > > Basically, I go through the process of converting > from unix to DOS > (using todos or unix2dos), then trying to run the fchk utility. I > have also tried simply opening the file using gview03 directly at > various stages of the process to no avail. Here is an output: > > > > > > C:\Users\Soren\Desktop>todos cysteineadiff.chk > > > > C:\Users\Soren\Desktop>formchk cysteineadiff > > Bad file opened by FileIO: Unit=2 I= 2 FPrev=40448 FCur= 0. > > FileIO: IOper= 9 IFilNo(1)= 2 Len= 0 IPos= 0 Q= > > 4476372 > > Error termination in NtrErr: > > NtrErr Called from FileIO. > > > > > > Thus, it seems this is larger than a simple unix/dos issue. Any ideas?? > > > > Thanks in advance. > > > > Soren N. Eustis > > Doctoral Candidate > > Department of Chemistry > > Johns Hopkins University > > 3400 N. Charles Street > > Baltimore, MD 21218 > > (W) 410-516-4675 > > (M) 410-925-5167 > > (fax) 410-516-8420 > > soren|jhu.edu > > > -- ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del País Vasco (UPV/EHU) Fac. Ciencia y Tecnología, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ******************************** --------------020603040903070702050701 Content-Type: text/x-vcard; charset=utf-8; name="pablo_vitoria.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="pablo_vitoria.vcf" begin:vcard fn;quoted-printable:Pablo Vitoria Garc=C3=ADa n;quoted-printable:Vitoria Garc=C3=ADa;Pablo org;quoted-printable:Universidad del Pa=C3=ADs Vasco (UPV/EHU);Servicios Generales de Rayos X adr;quoted-printable;quoted-printable:Barrio Sarriena s/n;;Facultad de Ciencia y Tecnolog=C3=ADa, edificio CD3;Leioa;Bizkaia;E-48940;Espa=C3=B1a email;internet:pablo.vitoria]~[ehu.es title;quoted-printable:T=C3=A9cnico SGIKer tel;work:946015334 tel;fax:946013500 tel;cell:660959834 version:2.1 end:vcard --------------020603040903070702050701-- From owner-chemistry@ccl.net Mon Apr 7 05:08:00 2008 From: "Uwe Huniar uwe.huniar * cosmologic.de" To: CCL Subject: CCL:G: Where might be my mistake in calculation by Turbomole using TDDFT? Message-Id: <-36656-080407044953-21980-/fsl0ai0OwPl1b9TgENvhA..server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 07 Apr 2008 10:50:11 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar/a\cosmologic.de] Dear Arvydas, Turbomole support requests can be addressed to turbomole_a_cosmologic_de or support_a_turbomole_com, questions to the Turbomole user community can be posted to the Turbomole user forum www.turbo-forum.com As Mariusz already wrote, Turbomole does ask for epsilon - this is the very first entry that is asked for in cosmoprep. COSMO is not fully implemented in the TDDFT part of Turbomole in the official release. The so called 'fast term' in the CPKS equations is missing. The developers version of Turbomole has a full implementation which will be included in the next version - but as far as I know, this term has only small contributions to the excited state energies. LanL2DZ: The basis set that is closest to LanL2DZ is def-SVP, but def-SVP is larger and has different ECPs. You can also download LanL2DZ from the EMSL site in Turbomole format. However, for TDDFT and hybrid functionals, a larger basis set should be more accurate, I would recommend to use def2-TZVP (def2-* are the latest, revised, triple-zeta basis sets from Karlsruhe, def-* are the older ones) for all elements up to Lr. > We have done solely specification of solvent but received very bad > Turbomole TDDFT B3LYP/LanL2DZ spectrum of [Ru(bpy)3]2+ in comparison > with right spectrum obtained by Gaussian03: Did you also compare to experiment? > Excited State 5: Singlet-E 2.7424 eV 452.09 nm f=0.0077 > Excited State 6: Singlet-E 2.7424 eV 452.09 nm f=0.0077 > Excited state symmetry could not be determined. > Excited State 7: Singlet-?Sym 2.8873 eV 429.41 nm f=0.1097 > Excited state symmetry could not be determined. > Excited State 8: Singlet-?Sym 2.8873 eV 429.41 nm f=0.1097 > (f - are bad in G03 for [Ru(bpy)3]2+) > > Where might be my mistake in calculation by Turbomole using TDDFT B3LYP > spectrum of [Ru(bpy)3]2+ using COSMO ? If you did switch on symmetry, please make sure to calculate the excited states of all irreps ($soes all ). Regards, Uwe From owner-chemistry@ccl.net Mon Apr 7 05:33:01 2008 From: "Arvydas Tamulis tamulis a mserv.itpa.lt" To: CCL Subject: CCL:G: Turbomole gives right oscillator strengths for [Ru(bpy)3]2+ Message-Id: <-36657-080407052501-3758-3LXKy+swEPI/4NpqR8+LFQ]~[server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 7 Apr 2008 12:24:43 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis\a/mserv.itpa.lt] Dear Uve and Colleagues from Turbomole support, Congratulations for Turbomole team! My calculated spectrum of TDDFT B3LYP gives right values of oscillator strengths for [Ru(bpy)3]2+ in vacuum. This is exceptional in comparison with other well known quantum chemical packages. What are the epsilon values for water and methanol molecules in cosmo Turbomole? I would like to calculate TDDFT B3LYP spectrum of [Ru(bpy)3]2+] in water or methanol solvents. Maybe needs to specify also other parameters in cosmo in the case if I wish to calculate spectra in water or in methanol solvents? With best regards, Arvydas On Mon, 7 Apr 2008, Uwe Huniar wrote: > Dear Arvydas, > > Turbomole support requests can be addressed to turbomole_a_cosmologic_de or > support_a_turbomole_com, questions to the Turbomole user community can be > posted to the Turbomole user forum www.turbo-forum.com > > As Mariusz already wrote, Turbomole does ask for epsilon - this is the very > first entry that is asked for in cosmoprep. > > COSMO is not fully implemented in the TDDFT part of Turbomole in the official > release. The so called 'fast term' in the CPKS equations is missing. The > developers version of Turbomole has a full implementation which will be > included in the next version - but as far as I know, this term has only small > contributions to the excited state energies. > > LanL2DZ: The basis set that is closest to LanL2DZ is def-SVP, but def-SVP is > larger and has different ECPs. You can also download LanL2DZ from the EMSL > site in Turbomole format. However, for TDDFT and hybrid functionals, a larger > basis set should be more accurate, I would recommend to use def2-TZVP (def2-* > are the latest, revised, triple-zeta basis sets from Karlsruhe, def-* are the > older ones) for all elements up to Lr. > >> We have done solely specification of solvent but received very bad >> Turbomole TDDFT B3LYP/LanL2DZ spectrum of [Ru(bpy)3]2+ in comparison with >> right spectrum obtained by Gaussian03: > > Did you also compare to experiment? > >> Excited State 5: Singlet-E 2.7424 eV 452.09 nm f=0.0077 >> Excited State 6: Singlet-E 2.7424 eV 452.09 nm f=0.0077 >> Excited state symmetry could not be determined. >> Excited State 7: Singlet-?Sym 2.8873 eV 429.41 nm f=0.1097 >> Excited state symmetry could not be determined. >> Excited State 8: Singlet-?Sym 2.8873 eV 429.41 nm f=0.1097 >> (f - are bad in G03 for [Ru(bpy)3]2+) >> >> Where might be my mistake in calculation by Turbomole using TDDFT B3LYP >> spectrum of [Ru(bpy)3]2+ using COSMO ? > > If you did switch on symmetry, please make sure to calculate the excited > states of all irreps ($soes all ). > > Regards, > > Uwe > From owner-chemistry@ccl.net Mon Apr 7 07:07:00 2008 From: "Mariusz Radon mariusz.radon%%gmail.com" To: CCL Subject: CCL:G: Where might be my mistake in calculation by Turbomole using TDDFT? Message-Id: <-36658-080407054215-15947-ZpwEgrQkDr84s6IaJPc1SA!=!server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=us-ascii Date: Mon, 07 Apr 2008 11:42:10 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon|*|gmail.com] "Arvydas Tamulis tamulis]=[mserv.itpa.lt" writes: > Where might be my mistake in calculation by Turbomole using TDDFT > B3LYP spectrum of [Ru(bpy)3]2+ using COSMO ? > I'm not the right person to answer this cos don't have experience with TDDFT+solvent. Anyway, if you get significantly different results from PCM (G03) and COSMO (Turbomole) I think that it's a bit suspicious. > By the way, I did not found the LanL2DZ basis set in Turbomole. > Which basis set is good for Ru atom in Turbomole?? You can always take the basis set (and ECP) from Gaussian and use them with Turbomole (see the format of ``basis'' file). You can even add the specification of LanL2DZ to your private basis set library (it's described somewhere in the manual). If you don't like to play with this you can find some relativistic-ECP basis sets for transition metals in the std Turbomole library, e.g. ecp-10-mdf etc. Though, I'm not sure if they are available also for the second-row metals. regards, Mariusz Radon -- Mariusz Radon Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Mon Apr 7 08:48:01 2008 From: "jamel-eddine.meslamani*_*ulp.u-strasbg.fr" To: CCL Subject: CCL: display probleme when executing a sybyl spl script Message-Id: <-36659-080407084349-13904-H05SZDKejGYUZNBMzIEFSA],[server.ccl.net> X-Original-From: jamel-eddine.meslamani]^[ulp.u-strasbg.fr Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 07 Apr 2008 14:43:33 +0200 MIME-Version: 1.0 Sent to CCL by: jamel-eddine.meslamani _ ulp.u-strasbg.fr Dear members, I have some variable's display problem when I execute an spl script, I got this as a result if I'd like to echo a variable: in the script: echo $sybyl_version echo $search_nrbonds terminal result after executing the script: SYBYL> ECHO SYBYL> ECHO After performing the systematic search,even if I try to use the variable, it seems to be misssing.The $sybyl_version is also undisplayed. Does anyone has an idea? Thank you in advance. MESLAMANI Jamel From owner-chemistry@ccl.net Mon Apr 7 09:22:01 2008 From: "Maxim Kholin maxim.kholin%x%q-pharm.com" To: CCL Subject: CCL: GPCR structure unavailable? We model it, dock on it or make customized docking tool for you. Message-Id: <-36660-080407084133-13633-mS9ApYfjGbfLXSKjJNKWxA:-:server.ccl.net> X-Original-From: "Maxim Kholin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="windows-1252"; reply-type=original Date: Mon, 7 Apr 2008 16:42:14 +0400 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin/./q-pharm.com] Dear Colleagues, Let me inform you about our new protein modeling technology and invite for collaborations and partnering. Quantum Pharmaceuticals introduced a novel technology platform able to produce protein models that can be used for docking and discovering hits based on it. We apply it for GPCRs and other proteins, which 3d structures are unavailable (e.g. hERG). The technology differs largely from what to the best of our knowledge is currently available for researchers. Instead of using QSAR discovery strategies, pharmacophore or homology modeling, we apply our core pure physics based technology to model a force field of the protein using the data known of the existing inhibitors of the same protein. Once we done we use this force field for virtual screening and identification of the absolutely novel strong inhibitors. These new inhibitors will not be similar to the inhibitor we used creating a protein's force field, neither in terms of chemical class, no in terms of pharmacophore. This is a main advantage of our approach. We look for the opportunities to enter collaborations, provide services or customized docking tools with original protein models inside. I will be glad to answer all questions. Maxim Kholin Business Development Director Quantum Pharmaceuticals Tel. +7(495) 150 8332 Fax +7(495) 156 156 1 6a Kosmonavta Volkova, off. # 606 Moscow, Russia maxim.kholin++q-pharm.com www.q-pharm.com www.q-lead.com From owner-chemistry@ccl.net Mon Apr 7 13:00:00 2008 From: "Mariusz Radon mariusz.radon*gmail.com" To: CCL Subject: CCL:G: projected vs. unprojected MPn benchmarks? Message-Id: <-36661-080407125627-25414-7PsYfBPBEsHUvUKgHqKZRw ~ server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=us-ascii Date: Mon, 07 Apr 2008 18:56:06 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon^gmail.com] Dear CCL-ers: I'm looking for benchmark studies on projected vs. unprojected MP2-MP4 for the UHF reference function. (By projected I mean the energies called ``PMPn'' in Gaussian output, while the unprojected are called ``UMPn''.) Could you please recommend me any publications systematically comparing the results from both approaches? Thanks in advance! best regards, Mariusz Radon -- Mariusz Radon Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Mon Apr 7 13:40:01 2008 From: "Close, David M. CLOSED(-)mail.etsu.edu" To: CCL Subject: CCL:G: projected vs. unprojected MPn benchmarks? Message-Id: <-36662-080407131334-808-r1xM0PObESvsYnftDmXmiw###server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 Apr 2008 13:13:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED++mail.etsu.edu] Mariusz: Yes I have done some PMP2 calculations of ionization potentials in the nucleic acid bases. For these cations the standard MP2 procedure is rather unreliable. But using the projected MP2 results gave rather good results. See for example JPCA 108, 10376-10379 (2004). Regards, Dave Close. -----Original Message----- > From: owner-chemistry]=[ccl.net [mailto:owner-chemistry]=[ccl.net]=20 Sent: Monday, April 07, 2008 12:56 PM To: Close, David M. Subject: CCL:G: projected vs. unprojected MPn benchmarks? Sent to CCL by: Mariusz Radon [mariusz.radon^gmail.com] Dear CCL-ers: I'm looking for benchmark studies on projected vs. unprojected MP2-MP4 for the UHF reference function. (By projected I mean the energies called ``PMPn'' in Gaussian output, while the unprojected are called ``UMPn''.) Could you please recommend me any publications systematically comparing the results from both approaches? Thanks in advance! best regards, Mariusz Radon --=20 Mariusz Radon Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon -=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 Mon Apr 7 14:10:01 2008 From: "Daniel Oberlin DOberlin%a%cambridgesoft.com" To: CCL Subject: CCL: OPLS/AA Validation Data Message-Id: <-36663-080407112709-11932-9286R8MfinECTAe7UrbDWQ(0)server.ccl.net> X-Original-From: "Daniel Oberlin" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C898BF.9894EDE6" Date: Mon, 7 Apr 2008 10:56:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Daniel Oberlin" [DOberlin%x%cambridgesoft.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C898BF.9894EDE6 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hello CCL, =20 I am interested in obtaining some reference data that can be used to validate an implementation of the OPLS/AA force-field. As an example of what I mean, a suite of data for the MMFF94 force field exists online: =20 http://www.ccl.net/cca/data/MMFF94/ =20 I have been unable to get such a data set for the OPLS/AA force field > from the authors, and I have been unsuccessful finding anything useful on the web or in any related papers that I know of. We would prefer not to have to buy an expensive piece of software merely for the purpose of generating this data. =20 Does anyone know how I can obtain some data in order to validate an implementation of the OPLS/AA force field? Sincerely, Dan Daniel M. Oberlin CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA 617.259.9959 dmo]=[cambridgesoft.com =20 =20 ------_=_NextPart_001_01C898BF.9894EDE6 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello CCL,

 

I am interested in obtaining some reference data = that can be used to validate an implementation of the OPLS/AA force-field.  As = an example of what I mean, a suite of data for the MMFF94 force field = exists online:

 

http://www.ccl.net/cca/data/= MMFF94/

 

I have been unable to get such a data set for the = OPLS/AA force field from the authors, and I have been unsuccessful finding anything = useful on the web or in any related papers that I know of.  We would prefer = not to have to buy an expensive piece of software merely for the purpose of = generating this data.

 

Does anyone know how I can obtain some data in = order to validate an implementation of the OPLS/AA force field?


Sincerely,

Dan

Daniel M. Oberlin
CambridgeSoft Corporation
100 CambridgePark Drive
Cambridge, MA 02140 USA
617.259.9959
dmo]=[cambridgesoft.com

 

------_=_NextPart_001_01C898BF.9894EDE6-- From owner-chemistry@ccl.net Mon Apr 7 19:05:01 2008 From: "Metwally, Essam emetwall::tripos.com" To: CCL Subject: CCL: display probleme when executing a sybyl spl script Message-Id: <-36664-080407153514-26300-lNRRgAoSyrTgHw28gOE41w###server.ccl.net> X-Original-From: "Metwally, Essam" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 07 Apr 2008 14:02:54 -0500 MIME-Version: 1.0 Sent to CCL by: "Metwally, Essam" [emetwall(0)tripos.com] Could you give me more detail on how you are running the script? -- Essam ---------------------------- Dr Essam Metwally Senior Development Scientist Tripos International emetwall/./tripos.com Tel +314 951 3260 ---------------------------- Announcing SYBYL 8.0 - with a fresh new look and feel. Install it today - you'll be glad you did! jamel-eddine.meslamani*_*ulp.u-strasbg.fr wrote: > > Sent to CCL by: jamel-eddine.meslamani _ ulp.u-strasbg.fr > Dear members, > > I have some variable's display problem when I execute an spl script, I > got this as a result if I'd like to echo a variable: > > in the script: > echo $sybyl_version > echo $search_nrbonds > > terminal result after executing the script: > SYBYL> ECHO > > SYBYL> ECHO > > After performing the systematic search,even if I try to use the > variable, it seems to be misssing.The $sybyl_version is also undisplayed. > Does anyone has an idea? > Thank you in advance. > > MESLAMANI Jamelhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > >