From owner-chemistry@ccl.net Fri Jul 28 00:18:00 2006 From: "Tapas Kar tapaskar,+,cc.usu.edu" To: CCL Subject: CCL:G: how to use different basis sets to calculate different atoms Message-Id: <-32284-060728001614-12254-JulwBGzs4E1ASkLE0T+sNw[A]server.ccl.net> X-Original-From: "Tapas Kar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Thu, 27 Jul 2006 22:16:10 -0600 MIME-Version: 1.0 Sent to CCL by: "Tapas Kar" [tapaskar a cc.usu.edu] Hi If you are using Gaussian, then use "Gen" in route card. Input example # HF Gen Title card Charge multiplicity Coordinates or Z-matrix (blank line) Co 0 lanl2dz+p **** 2-10 0 6-311+g* **** 16-30 0 6-31g **** H 0 6-31G **** (blank line) If you are using GAMESS, then you have to include basis functions after each atom line. Thanks Tapas -----Original Message----- > From: owner-chemistry!^!ccl.net [mailto:owner-chemistry!^!ccl.net] Sent: Thursday, July 27, 2006 9:40 PM To: Kar, Tapas Subject: CCL: how to use different basis sets to calculate different atoms Sent to CCL by: "Xiaocong Wang" [wise84{}mail.ustc.edu.cn] Thank you for pay attention to my question. I am doing a research on the Co compound, I want to use different basis sets on the different atoms. But in the compound, I need to use different basis set to calculate different C atoms, I do not know how to carry it on. The following is a model compound. co n 1 nco2 c 2 cn3 1 cnco3 o 1 oco4 2 ocon4 3 dih4 o 1 oco5 2 ocon5 3 dih5 c 1 cco6 2 ccon6 3 dih6 n 1 nco7 2 ncon7 3 dih7 c 1 cco8 2 ccon8 3 dih8 n 1 nco9 2 ncon9 3 dih9 c 9 cn10 1 cnco10 2 dih10 h 8 hc11 1 hcco11 2 dih11 h 8 hc12 1 hcco12 2 dih12 h 3 hc13 2 hcn13 1 dih13 h 6 hc14 7 hcn14 1 dih14 h 10 hc15 9 hcn15 1 dih15 c 3 cc16 2 ccn16 1 dih16 c 4 co17 1 coco17 2 dih17 c 17 cc18 4 cco18 1 dih18 c 18 cc19 17 ccc19 4 dih19 c 19 cc20 18 ccc20 17 dih20 c 16 cc21 3 ccc21 2 dih21 c 5 co22 1 coco22 2 dih22 c 6 cc23 7 ccn23 1 dih23 c 23 cc24 6 ccc24 7 dih24 c 24 cc25 23 ccc25 6 dih25 c 25 cc26 24 ccc26 23 dih26 c 22 cc27 5 cco27 1 dih27 c 9 cn28 1 cnco28 2 dih28 c 28 cc29 9 ccn29 1 dih29 c 29 cc30 28 ccc30 9 dih30 c 10 cc31 9 ccn31 1 dih31 c 7 cn32 1 cnco32 2 dih32 c 2 cn33 1 cnco33 4 dih33 c 33 cc34 2 ccn34 1 dih34 c 34 cc35 33 ccc35 2 dih35 c 35 cc36 34 ccc36 33 dih36 c 32 cc37 7 ccn37 1 dih37 c 8 cc38 1 ccco38 2 dih38 c 38 cc39 8 ccc39 1 dih39 h 24 hc40 23 hcc40 6 dih40 h 25 hc41 26 hcc41 27 dih41 h 26 hc42 27 hcc42 22 dih42 h 27 hc43 22 hcc43 5 dih43 h 31 hc44 10 hcc44 9 dih44 h 30 hc45 31 hcc45 10 dih45 h 29 hc46 28 hcc46 9 dih46 h 19 hc47 20 hcc47 21 dih47 h 20 hc48 21 hcc48 16 dih48 h 21 hc49 16 hcc49 3 dih49 h 28 hc50 9 hcn50 1 dih50 h 34 hc51 33 hcc51 2 dih51 h 35 hc52 36 hcc52 37 dih52 h 36 hc53 37 hcc53 32 dih53 h 37 hc54 32 hcc54 7 dih54 h 18 hc55 17 hcc55 4 dih55 h 38 hc56 8 hcc56 1 dih56 h 38 hc57 8 hcc57 1 dih57 h 39 hc58 38 hcc58 8 dih58 h 39 hc59 38 hcc59 8 dih59 h 39 hc60 38 hcc60 8 dih60 nco2 1.894681 cn3 1.315995 cnco3 125.282 oco4 1.895318 ocon4 94.762 dih4 -1.675 oco5 1.894269 ocon5 179.209 dih5 81.497 cco6 2.860777 ccon6 107.207 dih6 171.913 nco7 1.892278 ncon7 85.426 dih7 175.444 cco8 1.952326 ccon8 90.827 dih8 -90.135 nco9 2.109746 ncon9 92.127 dih9 84.823 cn10 1.351126 cnco10 115.659 dih10 -137.656 hc11 1.100346 hcco11 108.077 dih11 16.861 hc12 1.096165 hcco12 101.240 dih12 130.334 hc13 1.089970 hcn13 118.412 dih13 -179.130 hc14 1.090144 hcn14 118.373 dih14 174.643 hc15 1.081720 hcn15 114.933 dih15 -0.524 cc16 1.416309 ccn16 126.264 dih16 1.618 co17 1.310796 coco17 127.385 dih17 0.014 cc18 1.423268 cco18 118.661 dih18 -178.795 cc19 1.378071 ccc19 121.315 dih19 -178.699 cc20 1.415353 ccc20 121.114 dih20 -0.259 cc21 1.421988 ccc21 118.095 dih21 179.536 co22 1.311370 coco22 127.253 dih22 87.620 cc23 1.416554 ccn23 126.138 dih23 -6.030 cc24 1.421726 ccc24 118.173 dih24 -179.347 cc25 1.376730 ccc25 121.642 dih25 177.878 cc26 1.415178 ccc26 118.928 dih26 -0.283 cc27 1.423171 cco27 118.672 dih27 -177.770 cn28 1.348580 cnco28 125.260 dih28 41.584 cc29 1.392129 ccn29 122.281 dih29 -179.262 cc30 1.396016 ccc30 118.798 dih30 -0.041 cc31 1.392767 ccn31 121.786 dih31 179.407 cn32 1.412203 cnco32 112.822 dih32 7.087 cn33 1.413251 cnco33 112.759 dih33 176.100 cc34 1.401334 ccn34 126.228 dih34 -174.054 cc35 1.391787 ccc35 120.139 dih35 179.383 cc36 1.399072 ccc36 120.223 dih36 -0.680 cc37 1.401211 ccn37 126.033 dih37 173.050 cc38 1.523124 ccco38 119.342 dih38 -109.042 cc39 1.535759 ccc39 111.969 dih39 -173.750 hc40 1.087525 hcc40 118.225 dih40 -1.706 hc41 1.083754 hcc41 120.326 dih41 179.943 hc42 1.085852 hcc42 119.471 dih42 -179.798 hc43 1.083628 hcc43 117.003 dih43 -1.463 hc44 1.083348 hcc44 119.726 dih44 179.925 hc45 1.084519 hcc45 120.607 dih45 -179.955 hc46 1.083502 hcc46 119.985 dih46 179.933 hc47 1.085848 hcc47 119.401 dih47 179.591 hc48 1.083757 hcc48 120.742 dih48 179.874 hc49 1.087514 hcc49 118.219 dih49 0.959 hc50 1.083191 hcn50 116.284 dih50 0.632 hc51 1.083402 hcc51 120.771 dih51 0.370 hc52 1.084280 hcc52 120.113 dih52 179.202 hc53 1.084255 hcc53 119.699 dih53 179.701 hc54 1.083517 hcc54 120.661 dih54 -1.473 hc55 1.083596 hcc55 116.990 dih55 1.395 hc56 1.099233 hcc56 110.683 dih56 64.964 hc57 1.098171 hcc57 110.182 dih57 -52.646 hc58 1.096311 hcc58 110.729 dih58 59.588 hc59 1.097093 hcc59 111.597 dih59 179.899 hc60 1.096883 hcc60 110.883 dih60 -59.733 Co lanl2dz+p atom 2-10 6-311+g* atom 16-39 6-31g all the H atom 6-31g Thank you very much!http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jul 28 03:50:00 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas],[urv.cat" To: CCL Subject: CCL: Combining 3D-QSAR and experimental IC50 for guiding docking? Message-Id: <-32285-060728034743-9328-4QkiKnl5fBkbcGKRXCmRWA-x-server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Fri, 28 Jul 2006 09:47:09 +0200 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas ~ urv.cat] Dear CCL list members, we are now using protein-ligand complexes deposited in the PDB (same receptor crystallized with different inhibitors) to develop a 3D-QSAR function that could predict the IC50 value for ligands that have not been crystallized with this receptor. Moreover, we have IC50 experimental values for some inhibitors different than the ones that have been crystallized with the receptor. Therefore, I wonder if there is any docking software that can combine the IC50 experimental values and the 3D-QSAR function derived from the PDB complexes with that receptor to find the conformation of the ligands that give these experimental results. With many thanks in advances for your help Yours sincerely Gerard -- ============================= NOTE: NEW E-MAIL ============================ Dr. Gerard Pujadas Grup de recerca en Nutrigenòmica Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas#urv.cat Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Fri Jul 28 08:16:00 2006 From: "andrea spitaleri spitaleri.andrea~~hsr.it" To: CCL Subject: CCL: LJ parameters for Mn for using in MD Message-Id: <-32286-060727112935-1521-bAxbLDssIDRZca5nF5VRVA a server.ccl.net> X-Original-From: andrea spitaleri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 Jul 2006 16:29:34 +0200 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea(0)hsr.it] Hi all, I need to perform a MD on a protein with inside Mn2+ and I need the Lennard-Jones parameters for this ion. Does anyone has papers to suggest dealing with this issue? The idea is to use gromos ff, but in principle amber/charmm should also okay. Thanks in advance for any hints, Regards andrea -- ------------------------------- Andrea Spitaleri Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille]=[hsr.it o vai sul sito www.5xmille.org From owner-chemistry@ccl.net Fri Jul 28 09:20:00 2006 From: "David F. Green dfgreen*|*ams.sunysb.edu" To: CCL Subject: CCL: LJ parameters for Mn for using in MD Message-Id: <-32287-060728091821-2692-vT9UqPQ0dFwthJqJeFZvaw(a)server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 28 Jul 2006 09:18:01 -0400 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen(!)ams.sunysb.edu] Andrea, Before anything else, you might want to consider whether Mn2+ is the biologically relevant ion, or whether it was just used in the crystallography (very often Mn2+ will be substituted for Mg2+, as the heavier ion diffracts better). If this is the casee, there certainly should be parameters for Mg2+ in most biomolecular force fields, and you probably want to use that. Regards, David ======================================================================= David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Math Tower, Room 1-117 Voice: +1-631-632-9344 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================= andrea spitaleri spitaleri.andrea~~hsr.it wrote: > Sent to CCL by: andrea spitaleri [spitaleri.andrea(0)hsr.it] > > Hi all, > I need to perform a MD on a protein with inside Mn2+ and I need the Lennard-Jones parameters for > this ion. > Does anyone has papers to suggest dealing with this issue? The idea is to use gromos ff, but in > principle amber/charmm should also okay. > Thanks in advance for any hints, > > Regards > > andrea > From owner-chemistry@ccl.net Fri Jul 28 09:55:00 2006 From: "Noel O Boyle no228[a]cam.ac.uk" To: CCL Subject: CCL:G: how to use different basis sets to calculate different atoms Message-Id: <-32288-060728094621-22876-K7+Wqw5IaQWIEMvqqgcs8Q_._server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 28 Jul 2006 14:46:08 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228 ~~ cam.ac.uk] Just Gen isn't enough if using ECPs like LanL2DZ. You need to use GENECP instead of GEN, and to specify the ECP after the section described by Tapas. [...] H 0 6-31G **** (blank line) Co 0 lanl2dz+p [end of file] This is also described at the end of the webpage http://www.gaussian.com/g_ur/k_pseudo.htm (note that "GEN PSEUDO=READ" is the same as "GENECP"). (Editor, could I suggest the creation of a FAQ in relation to this question and also the question about the 2GB limit on Gaussian checkfiles) Regards, Noel On Fri, 2006-07-28 at 00:22 -0400, Tapas Kar tapaskar,+,cc.usu.edu wrote: > Sent to CCL by: "Tapas Kar" [tapaskar a cc.usu.edu] > Hi > If you are using Gaussian, then use "Gen" in route card. > Input example > # HF Gen > > Title card > > Charge multiplicity > Coordinates or Z-matrix > (blank line) > Co 0 > lanl2dz+p > **** > 2-10 0 > 6-311+g* > **** > 16-30 0 > 6-31g > **** > H 0 > 6-31G > **** > (blank line) > > > If you are using GAMESS, then you have to include basis functions after each > atom line. > > Thanks > Tapas From owner-chemistry@ccl.net Fri Jul 28 11:20:01 2006 From: "ReichertD===mir.wustl.edu" To: CCL Subject: CCL: Combining 3D-QSAR and experimental IC50 for guiding docking? Message-Id: <-32289-060728111738-19977-xS4O7mpTks+17w57CgAFfg++server.ccl.net> X-Original-From: ReichertD###mir.wustl.edu Content-type: multipart/related; Boundary="0__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF" Date: Fri, 28 Jul 2006 09:31:50 -0500 MIME-Version: 1.0 Sent to CCL by: ReichertD_._mir.wustl.edu --0__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF Content-type: multipart/alternative; Boundary="1__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF" --1__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: quoted-printable Gerard, Actually you really don't need the docking program to do this. We've published several papers on steroid binding where we split this into tw= o separate steps, docking using the programs (Gold) native scoring functi= ons to find the best docked conformation; then a 3D-QSAR (CoMFA) step to ra= nk the various conformations and ligands in terms of activity. Modern dock= ing programs are fast enough that you can dock a large number of unknowns/n= ovel compounds and then feed the conformations into your previously develope= d 3D-QSAR equations. This approach gives you a lot of flexibility in that= you can use whatever docking program works best with your system, and whate= ver QSAR technique you like best. hope that helps, -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd]|[wustl.edu http://scoobie.wustl.edu/ voice: (314) 362-8461 fax: (314) 362-9940 = "D.BIO- Gerard = Pujadas = gerard.pujadas],[ = To urv.cat" "Reichert, David E. " = = ccl.net> = cc Sent by: = owner-chemistry]|[c Subj= ect cl.net CCL: Combining 3D-QSAR and = experimental IC50 for guiding = docking? = 07/28/2006 03:28 = AM = = = Please respond to = "CCL Subscribers" = = = = Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas ~ urv.cat] Dear CCL list members, we are now using protein-ligand complexes deposited in the PDB (same receptor crystallized with different inhibitors) to develop a 3D-QSAR function that could predict the IC50 value for ligands that have not been crystallized with this receptor. Moreover, we have IC50 experimental values for some inhibitors different than the ones that have been crystallized with the receptor. Therefore, I wonder if there is any docking software that can combine the IC50 experimental values and the 3D-QSAR function derived from the PDB complexes with that receptor to find the conformation of the ligands that give these experimental results. With many thanks in advances for your help Yours sincerely Gerard -- =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D NOTE: NEW E-MAIL =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Gerard Pujadas Grup de recerca en Nutrigen=F2mica Dept. Bioqu=EDmica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas[*]urv.cat Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel=B7l=ED Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D -=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 chang= ehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= Search Messages: http://www.ccl.net/htdig (login: ccl, Password: searc= h)http://www.ccl.net/spammers.txt-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= + = --1__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF Content-type: text/html; charset=ISO-8859-1 Content-Disposition: inline Content-transfer-encoding: quoted-printable

Gerard,
Actually you really don't need the docking program to do this. We've pu= blished several papers on steroid binding where we split this into two = separate steps, docking using the programs (Gold) native scoring functi= ons to find the best docked conformation; then a 3D-QSAR (CoMFA) step t= o rank the various conformations and ligands in terms of activity. Mode= rn docking programs are fast enough that you can dock a large number of= unknowns/novel compounds and then feed the conformations into your pre= viously developed 3D-QSAR equations. This approach gives you a lot of f= lexibility in that you can use whatever docking program works best with= your system, and whatever QSAR technique you like best.
hope that helps,
-david
David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd]|[wustl.edu
http://scoobie.wustl.edu/
=
voice: (314) 362-8461
fax: (314) 362-9940
3D"Inactive=

          "D.BIO- Gerard Pujadas gerard.pujadas],[ur= v.cat" <owner-chemistry]|[ccl.net>=
          Sent by: owner-chemistry]|[ccl.net

          07/28/2006 03:28 AM =
          Please respond to
          "CCL Subscribers" <chemistry]|[ccl.net>

=

To
3D""
"Reichert, David E. " <reichertd]|[= mir.wustl.edu>

cc
3D""

Subject
3D""
CCL: Combining 3D-QSAR and experimental IC50 for guidi= ng docking?
=3D""3D""<= /td>

Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas ~= urv.cat]

Dear CCL list members,

we are now using protein-ligand complexes
deposited in the PDB (same receptor crystallized
with different inhibitors) to develop a 3D-QSAR
function that could predict the IC50 value for
ligands that have not been crystallized with this
receptor.

Moreover, we have IC50 experimental values for
some inhibitors different than the ones that have
been crystallized with the receptor. Therefore, I
wonder if there is any docking software that can
combine the IC50 experimental values and the
3D-QSAR function derived from the PDB complexes
with that receptor to find the conformation of
the ligands that give these experimental results.

With many thanks in advances for your help

Yours sincerely

Gerard

--
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D NOTE: NEW E-MAIL =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dr. Gerard Pujadas
Grup de recerca en Nutrigen=F2mica
Dept. Bioqu=EDmica i Biotecnologia           r= oom 106
Campus de Sant Pere Sescelades    e-mail: gerard.pujadas= [*]urv.cat
Univ. Rovira i Virgili              =       phone: 34-977 559565
C/ Marcel=B7l=ED Domingo             &nbs= p;         fax: 34-977 558232
43007 Tarragona (CATALONIA)
State: Spain (European Union)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D



-=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 chang= e      http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /tt>
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /tt>
     http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.net/jo= bs 
Conferences: http://server.ccl.net/chemistry/announcements/con= ferences/

Search Messages: http://w= ww.ccl.net/htdig  (login: ccl, Password: search)
     http://www.ccl.net/spammers.txt

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

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +




= --1__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF-- --0__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF Content-type: image/gif; name="graycol.gif" Content-Disposition: inline; filename="graycol.gif" Content-ID: <10__=09BBFB2ADFDCB2BF8f9e8a]|[msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhEAAQAKECAMzMzAAAAP///wAAACH5BAEAAAIALAAAAAAQABAAAAIXlI+py+0PopwxUbpu ZRfKZ2zgSJbmSRYAIf4fT3B0aW1pemVkIGJ5IFVsZWFkIFNtYXJ0U2F2ZXIhAAA7 --0__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF Content-type: image/gif; name="pic13648.gif" Content-Disposition: inline; filename="pic13648.gif" Content-ID: <20__=09BBFB2ADFDCB2BF8f9e8a]|[msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhWABDALP/AAAAAK04Qf79/o+Gm7WuwlNObwoJFCsoSMDAwGFsmIuezf///wAAAAAAAAAA AAAAACH5BAEAAAgALAAAAABYAEMAQAT/EMlJq704682770RiFMRinqggEUNSHIchG0BCfHhOjAuh EDeUqTASLCbBhQrhG7xis2j0lssNDopE4jfIJhDaggI8YB1sZeZgLVA9YVCpnGagVjV171aRVrYR RghXcAGFhoUETwYxcXNyADJ3GlcSKGAwLwllVC1vjIUHBWsFilKQdI8GA5IcpApeJQt8L09lmgkH LZikoU5wjqcyAMMFrJIDPAKvCFletKSev1HBw8KrxtjZ2tvc3d5VyKtCKW3jfz4uMKmq3xu4N0nK BVoJQmx2LGVOmrqNjjJf2hHAQo/eDwJGTKhQMcgQEEAnEjFS98+RnW3smGkZU6ncCWav/4wYOnAI TihRL/4FEwbp28BXMMcoscQCVxlepL4IGDSCyJyVQOu0o7CjmLN50OZlqWmyFy5/6yBBuji0AxFR M00oQAqNIstqI6qKHUsWRAEAvagsmfUEAImyxgbmUpJk3IklNUtJOUAVLoUr1+wqDGTE4zk+T6FG uQb3SizBCwatiiUgCBN8vrz+zFjVyQ8FWkOlg4NQiZMB5QS8QO3mpOaKnL0Z2EKvNMSILEThKhCg zMKPVxYJh23qm9KNW7pArPynMqZDiErsTMqI+LRi3QAgkFUbXpuFKhSYZALd0O5RKa2z9EYKBbpb qxIKsjUPRgD7I2XYV6wyrOw92ykExP8NW4URhknC5dKGE4v4NENQj2jXjmfNgOZDaXb5glRmXQ33 YEWQYNcZFnrYcIQLNzyTFDQNkXIff0ExVlY4srziQk43inZgL4rwxxINMvpFFAz1KOODHiu+4aEw NEjFl5B3JIKWKF3k6I9bfUGp5ZZcdunll5IA4cuHvQQJ5gcsoCWOOUwgltIwAKRxJgbIkJAQZEq0 2YliZnpZZ4BH3CnYOXldOUOfQoYDqF1LFHbXCrO8xmRsfoXDXJ6ChjCAH3QlhJcT6VWE6FCkfCco CgrMFsROrIEX3o2whVjWDjoJccN3LdggSGXLCdLEgHr1lyU3O3QxhgohNKXJCWv8JQr/PDdaqd6w 2rj1inLiGeiCJoDspAoQlYE6QWLSECehcWIYxIQES6zhbn1iImTHEQyqJ4eIxJJoUBc+3CbBuwZE V5cJPPkIjFDdeEabQbd6WgICTxiiz0f5dBKquXF6k4senwEhYGnKEFJeGrxUZy8dB8gmAXI/sPvH ESfCwVt5hTgYiqQqtdRNHQIU1PJ33ZqmzgE90OwLaoJcnMop1WiMmgkPHQRIrwgFuNV90A3doNKT mrKIN07AnGcI9BQjhCBN4RfA1qIZnMqorJCogKfGQnxSCDilTVIA0yl5ciTovgLuBDKFUDE9aQcw 9SA+rjSNf9/M1gxrj6VwDTS0IUSElMzBfsj0NFXR2kwsV1A5IF1grLgLL/r1R40BZEnuBWgmQEyb jqRwSAt6bqMCOFkvKFN2GPPkUzIm/SCF8z8pVzpbjVnMsy0vOr1hw3SaSRUhpY09v0z0J1FnwzPl fmh+xl4WtR0zGu24I4KbMQm3lnVu2oNWxI9W/lcyzA+mCKF4DBikxb/+UWtOGRiFP8qEwAayIgIA Ow== --0__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF Content-type: image/gif; name="ecblank.gif" Content-Disposition: inline; filename="ecblank.gif" Content-ID: <30__=09BBFB2ADFDCB2BF8f9e8a]|[msnotes.wustl.edu> Content-transfer-encoding: base64 R0lGODlhEAABAIAAAAAAAP///yH5BAEAAAEALAAAAAAQAAEAAAIEjI8ZBQA7 --0__=09BBFB2ADFDCB2BF8f9e8a93df938690918c09BBFB2ADFDCB2BF-- From owner-chemistry@ccl.net Fri Jul 28 16:42:00 2006 From: "Monjardet, Veronique vmonjard:tripos.com" To: CCL Subject: CCL: Combining 3D-QSAR and experimental IC50 for guiding docking? Message-Id: <-32290-060728102935-16725-uhQ/2i1PnZfP2RtelKC9Vw{}server.ccl.net> X-Original-From: "Monjardet, Veronique" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 28 Jul 2006 08:44:20 -0500 MIME-Version: 1.0 Sent to CCL by: "Monjardet, Veronique" [vmonjard(_)tripos.com] Dear Gerard, I don't know what exactely your are expecting but I could suggest you to use a pharmacophorique approche instead of a docking one in order to find the good conformation of your ligand related to the IC50. If you need further informations, please do not heistate to contact me. Have a nice day, Veronique vmonjard__tripos.com -----Original Message----- > From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] Sent: vendredi 28 juillet 2006 10:07 To: Monjardet, Veronique Subject: CCL: Combining 3D-QSAR and experimental IC50 for guiding docking? Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas ~ urv.cat] Dear CCL list members, we are now using protein-ligand complexes deposited in the PDB (same receptor crystallized with different inhibitors) to develop a 3D-QSAR function that could predict the IC50 value for ligands that have not been crystallized with this receptor. Moreover, we have IC50 experimental values for some inhibitors different than the ones that have been crystallized with the receptor. Therefore, I wonder if there is any docking software that can combine the IC50 experimental values and the 3D-QSAR function derived from the PDB complexes with that receptor to find the conformation of the ligands that give these experimental results. With many thanks in advances for your help Yours sincerely Gerard -- ============================= NOTE: NEW E-MAIL ============================ Dr. Gerard Pujadas Grup de recerca en Nutrigenòmica Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas[*]urv.cat Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) ===========================================================================http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jul 28 17:17:00 2006 From: "Keith Tobias Butler keeeto2000-#-yahoo.co.uk" To: CCL Subject: CCL:G: Implimenting RM1 Method In Gaussian 03? Message-Id: <-32291-060728110613-18764-hfbQIQA7ww8bXQiv1u9l6Q||server.ccl.net> X-Original-From: "Keith Tobias Butler" Date: Fri, 28 Jul 2006 11:06:13 -0400 Sent to CCL by: "Keith Tobias Butler" [keeeto2000]^[yahoo.co.uk] Dear Members, I am trynig to impliment the RM1 reparameterization in Gaussian 03. I have changed the parameters in the utilam.F file of Gaussian, simply replacing values verbatim with the values quoted in the paper. I have recompiled gaussian and run some test calculations, but the values I obtain are different (sometimes wildly) from the values quoted in the additional material provided with the paper. I wonder has somebody else succesfully implimented RM1 in Gaussian, and can you tell me if maybe I have to change some other source files apart from utilam.F. Thank You for your time, Keith. From owner-chemistry@ccl.net Fri Jul 28 17:52:00 2006 From: "=?ISO-8859-1?Q?Annette_H=F6glund?= hoeglund,,schrodinger.com" To: CCL Subject: CCL: seeking free chemical geometry builder software in Linux Message-Id: <-32292-060728154238-6925-TL7fmqAOlz/iGNJ0A+nVDw*|*server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Annette_H=F6glund?= Date: Fri, 28 Jul 2006 21:01:17 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Annette_H=F6glund?= [hoeglund::schrodinger.com] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Provags-ID: kundenserver.de abuse!A!kundenserver.de login:b8f07107e4b9d70e7bcbb3b2fc5f32fb X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.1.3 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 3.1.3 (2006-06-01) on server.ccl.net Hi JunJun Liu and all other CCL subscribers, Schrodinger provides Maestro at no charge to academic users. Maestro is an all-purpose molecular modeling environment that includes a versatile builder with the capabilities you describe and more. Maestro's easy-to-use design is the front end to many other powerful tools. To register and download your own copy, please visit https://www.schrodinger.com/getmaestro. Best Regards, Annette Höglund > Sent to CCL by: "JunJun Liu" [ljjlp03||gmail.com] > Hi all, > I'm wondering if there's a free chemical geometry builder software > under >Linux. I hope this builder can handle two seperate molecules > >respectively in one window. For example, with molecule A being fixed, > >molecule B can be rotated/translated to close to molecule A in a > desired >orientation. Any recommendations are welcome and appreciated! > Regards! > Liu > -- > JunJun Liu > College of Chemistry > Central China Normal University > WuHan 430079 > P.R. China -- ________________________________________________________________ Annette Höglund, PhD, Schrödinger, Account Manager [t] +49 621 43855 172 [f] +49 621 43855 555 [e] hoeglund(at)schrodinger.com http://www.schrodinger.com Dynamostr. 13, 68165 Mannheim, Germany From owner-chemistry@ccl.net Fri Jul 28 18:27:00 2006 From: "matthew john tassell mtassell###gmail.com" To: CCL Subject: CCL:G: ci imput file problem Message-Id: <-32293-060728112417-24703-xS4O7mpTks+17w57CgAFfg(-)server.ccl.net> X-Original-From: "matthew john tassell" Date: Fri, 28 Jul 2006 11:24:17 -0400 Sent to CCL by: "matthew john tassell" [mtassell*|*gmail.com] hi, ive just started to get to know gaussian 03 and have been looking at vanadium oxide. ive been performing scans with different basis sets and methods. i tried the basis set sdd with ci and found that the highest level of basis set that appeared in the output file was mp3? below is my imput file, just in case i am writing it wrong. any help would be very gratefully received. matt %NProcShared=2 %NProc=2 %chk=quartet.chk P CI/SDD scan GFINPUT IOP(6/7=3) 6D 10F vanadium oxide 0 4 o v 1 ov2 ov2 1.0 50 0.1 From owner-chemistry@ccl.net Fri Jul 28 19:35:00 2006 From: "Daria Khvostichenko dkhvosti%x%uiuc.edu" To: CCL Subject: CCL: transition state optimization for ethylene Message-Id: <-32294-060728170237-31388-iPxnEyliMUm+MFvZ1yhEEQ]*[server.ccl.net> X-Original-From: "Daria Khvostichenko" Date: Fri, 28 Jul 2006 17:02:36 -0400 Sent to CCL by: "Daria Khvostichenko" [dkhvosti|,|uiuc.edu] Dear CCL subscribers, Does anybody know how to obtain a transition state structure for ethylene rotation about the double bond? I have tried QST2 and QST3 optimizations; they converge to the same structure, but frequency analysis of the output structure does not show any imaginary frequencies. Berny TS optimization does not converge (it runs into structures with two imaginary frequencies). When I used opt=(ts,noeigentest,calcfc,EF) it converged to the same structure as QST2 and QST3. I did calculations with ub3lyp/6-31g(d) and ub3lyp/6-311(d,p) methods; the results are more or less identical for both basis sets. Thank you in advance, Daria dkhvosti,,uiuc.edu Daria Khvostichenko Postdoctoral Research Associate Department of Chemistry Roger Adams Laboratory, 23-5 600 S. Mathews ave., MC-712 University of Illinois Urbana, IL 61801 217-244-2102; 217-244-3186 (fax)