From owner-chemistry@ccl.net Wed Sep 16 09:34:01 2009 From: "Babak Khalili Hadad khalili.babak : gmail.com" To: CCL Subject: CCL:G: readwa-lseekm error i Gaussian 98 Message-Id: <-40256-090916093331-20448-pQO9nys3N/oSUC/yvGuDIQ ~ server.ccl.net> X-Original-From: "Babak Khalili Hadad" Date: Wed, 16 Sep 2009 09:33:27 -0400 Sent to CCL by: "Babak Khalili Hadad" [khalili.babak[#]gmail.com] Dear Subscribers, I have done a calculation on Gaussian98 under windows to hold freq analysis. Unfortunately, the error of wrtitewa occurs all times. I increases the memory by $FREQMEM and again the writewa appeared, again I do increase of %mem=100mw but the "readwa-lseekm" is appeared now. May you lead me to solve this problem? You can see the following as an example. Best regards, Babak Khalili Inv2: IOpt= 1 Iter= 1 AM= 7.50D-16 Conv= 1.00D-12. Inverted reduced A of dimension 42 with in-core refinement. G2DrvN: will do 132 atoms at a time, making 1 passes doing MaxLOS=1. FoFDir used for L=0 through L=1. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. Integrals replicated using symmetry in FoFDir. MinBra= 0 MaxBra= 1 Meth= 1. IRaf= 0 NMat= 399 IRICut= 82 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. Raff turned off since only 32.11% of shell-pairs survive. There are 399 degrees of freedom in the 1st order CPHF. 396 vectors were produced by pass 0. AX will form 396 AO Fock derivatives at one time. 396 vectors were produced by pass 1. readwa-lseekm From owner-chemistry@ccl.net Wed Sep 16 12:36:01 2009 From: "=?EUC-KR?B?sei8vMiv?= shkim:+:bmdrc.org" To: CCL Subject: CCL: Ligand based virtual screening and drug design Message-Id: <-40257-090916050226-24799-mbsDk/pSSeJCx7PyT6urxA,server.ccl.net> X-Original-From: =?EUC-KR?B?sei8vMiv?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Sep 2009 13:11:01 +0900 MIME-Version: 1.0 Sent to CCL by: =?EUC-KR?B?sei8vMiv?= [shkim * bmdrc.org] My opinion is this program is good for LBDD. Pharmacophore based virtual screening : 3D QSAR Pharmacophore module and Multiconformer database : Discovery studio (Accelrys) www.accelrys.org 2009/9/15 Werner K werner.schroedinger(-)googlemail.com : > > Sent to CCL by: "Werner =A0K" [werner.schroedinger a googlemail.com] > Hi, > > what is in your opinion the best software packages for ligand based virtu= al screening and drug design? > > Thanks > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Sep 16 13:11:00 2009 From: "Aniko Simon aniko,+,simbiosys.ca" To: CCL Subject: CCL: Molecule Image Dataset REQUIRED Message-Id: <-40258-090916124145-2518-sX/eMn0dyyYa4gtQgdPZgg_+_server.ccl.net> X-Original-From: "Aniko Simon" Date: Wed, 16 Sep 2009 12:41:42 -0400 Sent to CCL by: "Aniko Simon" [aniko(_)simbiosys.ca] Noureddin, Prof. Peter Johnson's group at the University of Leeds, and his affiliates SimBioSys, Inc. and Keymodule Ltd. are pioneers in this field (i.e. OCSR - Optical Chemical Structure Recognition) since the early 90'ies. We do believe that having a publicly available benchmarking test set is a great value to the scientific community. Please read this recent blog post: http://www.simbiosys.ca/blog/2009/06/15/clide-for-converting-structure-images-to-structure-files/ which refers to the recent publication: Aniko T. Valko, A. Peter Johnson: CLiDE Pro: The Latest Generation of CLiDE, a Tool for Optical Chemical Structure Recognition J. Chem. Inf. Model., 2009, 49 (4), pp 780-787 DOI: 10.1021/ci800449t We offer two OCSR benchmarking test sets (the latest one is referred in the above paper), they are both posted on our web-site and freely available: http://www.simbiosys.ca/clide/validation.html Best wishes, Aniko -- Aniko Simon, Ph.D. | SimBioSys Inc. | Tel: 1-416-741-4263 http://www.simbiosys.ca/ | blog: http://www.simbiosys.ca/blog/ On September 14, 2009, Noureddin Sadawi n.sadawi|*|gmail.com wrote: > Sent to CCL by: "Noureddin Sadawi" [n.sadawi%gmail.com] > Dear all, > I am looking for a freely available molecule image dataset. I am looking > for scanned images as I am developing a system to extract SMILES notation > from such images. > > Any help is appreciated, > > Thanks > From owner-chemistry@ccl.net Wed Sep 16 14:10:01 2009 From: "Jean-Christophe Poully poully~~galilee.univ-paris13.fr" To: CCL Subject: CCL:G: readwa-lseekm error i Gaussian 98 Message-Id: <-40259-090916124842-5599-Uzea3R6gWJ8FYynUGAws5Q-,-server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Wed, 16 Sep 2009 18:48:29 +0200 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully a galilee.univ-paris13.fr] Try typing "%mem=3DXGB" in which you replace X by=20 the maximum amount of memory (RAM) your computer=20 can afford. If it doesn't work it means you=20 cannot achieve the calculation and you have to decrease the level of theory. Hope this helps, JC Poully At 15:33 16/09/2009, you wrote: >Sent to CCL by: "Babak Khalili Hadad" [khalili.babak[#]gmail.com] >Dear Subscribers, > >I have done a calculation on Gaussian98 under=20 >windows to hold freq analysis. Unfortunately,=20 >the error of wrtitewa occurs all times. >I increases the memory by $FREQMEM and again the=20 >writewa appeared, again I do increase of=20 >%mem=3D100mw but the "readwa-lseekm" is appeared=20 >now. May you lead me to solve this problem? >You can see the following as an example. > >Best regards, >Babak Khalili > > >Inv2: IOpt=3D 1 Iter=3D 1 AM=3D 7.50D-16 Conv=3D 1.00D-12. > Inverted reduced A of dimension 42 with in-core refinement. > G2DrvN: will do 132 atoms at a time, making 1 passes doing MaxLOS=3D1= . > FoFDir used for L=3D0 through L=3D1. > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > Integrals replicated using symmetry in FoFDir. > MinBra=3D 0 MaxBra=3D 1 Meth=3D 1. > IRaf=3D 0 NMat=3D 399 IRICut=3D 82=20 > DoRegI=3DT DoRafI=3DT ISym2E=3D 2 JSym2E=3D2. > Raff turned off since only 32.11% of shell-pairs survive. > There are 399 degrees of freedom in the 1st order CPHF. > 396 vectors were produced by pass 0. > AX will form 396 AO Fock derivatives at one time. > 396 vectors were produced by pass 1. > readwa-lseekm > > > >-=3D This is automatically added to each message by the mailing script =3D-Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Wed Sep 16 16:24:00 2009 From: "Sahan Thanthiriwatte sahanchem#,#gmail.com" To: CCL Subject: CCL:G: Counterpoise Correction Message-Id: <-40260-090914130229-10363-Q/fVjLAIDRh+8aASj8CpcQ .. server.ccl.net> X-Original-From: Sahan Thanthiriwatte Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-7 Date: Mon, 14 Sep 2009 12:13:48 -0400 MIME-Version: 1.0 Sent to CCL by: Sahan Thanthiriwatte [sahanchem^^^gmail.com] HI Uttama, You may find nice tutorial about computing non-covalent interactions on following article. ``Computations of Noncovalent =F0 Interactions,'' C. D. Sherrill, in Reviews in Computational Chemistry, Vol. 26, edited by K. B. Lipkowitz and T. R. Cundari (Wiley, New York, 2009), pages 1-38 Regards, -Sahan- /*---------------------------*/ K. Sahan Thanthiriwatte On Mon, Sep 14, 2009 at 6:23 AM, Uttama Mukherjee uttamachemistry%%gmail.com wrote: > > Sent to CCL by: "Uttama Mukherjee" [uttamachemistry ~ gmail.com] > My problem is- > Could you please elaborate the calculation of counterpoise co= rrection (Boys-Bernardi approach) for the evaluation of binding energy or i= nteraction energy of species like A and B interacting to give AB? > I had come across a Ph.D. thesis entitled"Interaction and Ap= plication Of Basis Set Superposition Error-Correction Schemes to the Theore= tical Modelling of Weak Intermolecular Interactions"(university of Girona)w= here an equation for the counterpoise-corrected interaction energy > is given. But my question is how to implement it via Gaussian03 suite of = programmes? > Kindly clarify the equation and suggest how to apply it thro= ugh G03 computationally for a particular interacting species. > > Uttama Mukherjee > uttamachemistry-,-gmail.c= om > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > From owner-chemistry@ccl.net Wed Sep 16 17:07:01 2009 From: "Pedro Salvador pedro.salvador:+:udg.edu" To: CCL Subject: CCL:G: Counterpoise Correction Message-Id: <-40261-090916170332-1472-Hp6hDAVydeF86+p5+KCpxw!=!server.ccl.net> X-Original-From: Pedro Salvador Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 16 Sep 2009 21:56:27 +0200 MIME-Version: 1.0 Sent to CCL by: Pedro Salvador [pedro.salvador=-=udg.edu] Hi, it is already implemented in Gaussian03. Just check on keyword "Counterpoise". http://www.gaussian.com/g_tech/g_ur/k_counterpoise.htm Regards Pedro Uttama Mukherjee uttamachemistry%%gmail.com wrote: > Sent to CCL by: "Uttama Mukherjee" [uttamachemistry ~ gmail.com] > My problem is- > Could you please elaborate the calculation of counterpoise correction (Boys-Bernardi approach) for the evaluation of binding energy or interaction energy of species like A and B interacting to give AB? > I had come across a Ph.D. thesis entitled"Interaction and Application Of Basis Set Superposition Error-Correction Schemes to the Theoretical Modelling of Weak Intermolecular Interactions"(university of Girona)where an equation for the counterpoise-corrected interaction energy > is given. But my question is how to implement it via Gaussian03 suite of programmes? > Kindly clarify the equation and suggest how to apply it through G03 computationally for a particular interacting species. > > Uttama Mukherjee > uttamachemistry-,-gmail.com> From owner-chemistry@ccl.net Wed Sep 16 22:30:01 2009 From: "Andrei Leitao ierdna[#]ig.com.br" To: CCL Subject: CCL: Ligand based virtual screening and drug design Message-Id: <-40262-090915115734-32696-fcRFIQgMr8yUZ8OxQLZjYA^server.ccl.net> X-Original-From: Andrei Leitao Content-Type: multipart/alternative; boundary=001636ed7070d7d24e04739f742f Date: Tue, 15 Sep 2009 12:30:03 -0300 MIME-Version: 1.0 Sent to CCL by: Andrei Leitao [ierdna::ig.com.br] --001636ed7070d7d24e04739f742f Content-Type: text/plain; charset=ISO-8859-1 Hi, For me, the OpenEye set is the best one, with very good results using ROCS for 3D similarity. Brood appears to be interesting for bioisosterism, but I did not try it yet. Filter is a good tool for reducing the amount of molecules in huge databanks by means of simple (and useful) rules. Omega generates quite good conformations in a straightforward way. Atomic charges can be calculated with Quacpac. These programs can be used together, without any costs for academics. Website: http://www.eyesopen.com Best, Andrei 2009/9/15 Werner K werner.schroedinger(-)googlemail.com < owner-chemistry\a/ccl.net> > > Sent to CCL by: "Werner K" [werner.schroedinger a googlemail.com] > Hi, > > what is in your opinion the best software packages for ligand based virtual > screening and drug design? > > Thanks> > > --001636ed7070d7d24e04739f742f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable =A0Hi,

=A0For me, the OpenEye set is the best one, with very good re= sults using ROCS for 3D similarity.
=A0Brood appears to be interesting f= or bioisosterism, but I did not try it yet.
=A0Filter is a good tool for= reducing the amount of molecules in huge databanks by means of simple (and= useful) rules.
=A0Omega generates quite good conformations in a straightforward way.
= =A0Atomic charges can be calculated with Quacpac.

=A0These programs = can be used together, without any costs for academics.
=A0Website: http://www.eyesopen.com


=A0Best,

=A0Andrei



2009/9/15 Werner K werner.schroedinger(-)googlemail.com <owner-chemistry\a/ccl.net>

Sent to CCL by: "Werner =A0K" [werner.schroedinger a googlemail.com]
Hi,

what is in your opinion the best software packages for ligand based virtual= screening and drug design?

Thanks



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