From chemistry-request@ccl.net Fri Jul 4 23:30:21 2003 Received: from web15208.mail.bjs.yahoo.com (web15208.mail.bjs.yahoo.com [202.3.77.138]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h653UCqe012666 for ; Fri, 4 Jul 2003 23:30:13 -0400 Message-ID: <20030705033010.90025.qmail[at]web15208.mail.bjs.yahoo.com> Received: from [218.241.68.19] by web15208.mail.bjs.yahoo.com via HTTP; Sat, 05 Jul 2003 11:30:10 CST Date: Sat, 5 Jul 2003 11:30:10 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: Re: CCL:About Parabolic fields in CoMFA To: Fabien Fontaine Cc: CCL In-Reply-To: <3F0543AB.50207[at]imim.es> MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Thank you very much for your response to my question. I have found a little infomation about parabolic fileds in the QSAR manual of Tripos' Sybyl 6.7. It said that "Parabolic fields are those in which the magnitude of a standard steric and/or electrostatic field at each lattice point has been squared; the original sign of the energy is retained." I am not sure about the meaning of parabolic fields. It seems that the value of the parabolic fields is only the squared value of Tripos standard fields. Why the parabolic field could improve the quality of QSAR model? Thanks again for your reply. Regards, Jinsong --- Fabien Fontaine : > I do not know what are the parabolic fields of CoMFA > but I think that > there is no problem of mixing 2 differents types of > molecular field in > one PLS model, because PLS takes care of the > correlation between the > variables. > However I guess that for simplicity, it is better to > use only one method > (CoMFA or CoMSIA) unless the combinations of both > methods give you a > significant improvement over the use of a single > one. > > > Regards, > Fabien > > > -- > Fabien Fontaine > Engineer in Biotechnology > Computer-Assisted Drug Design Laboratory > Research Group on Biomedical Informatics (GRIB) - > IMIM/UPF > > Passeig Maritim de la Barceloneta, 37-49 Tel: +34 93 > 224 08 94 > E-08003 Barcelona (Spain) Fax: +34 93 224 > 08 74 > e-mail: ffontaine~at~imim.es http://www.imim.es/grib > > > > _________________________________________________________ Do You Yahoo!? 9zDZ5gSJSC;'74@,;x5w2i@-?*a!D; http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.tech.yahoo.com/zhuanti/laji/index.html From chemistry-request@ccl.net Fri Jul 4 18:15:55 2003 Received: from mail.uh.edu (SanJacinto.Mail.UH.EDU [129.7.69.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h64MFtqe008619 for ; Fri, 4 Jul 2003 18:15:55 -0400 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HHI00501TUCHW~at~mail.uh.edu> for chemistry~at~ccl.net; Fri, 4 Jul 2003 17:15:48 -0500 (CDT) Received: from localhost (Colorado.Mail.UH.EDU [129.7.69.103]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HHI00551TUCBG~at~mail.uh.edu> for chemistry~at~ccl.net; Fri, 04 Jul 2003 17:15:48 -0500 (CDT) Date: Fri, 04 Jul 2003 17:15:48 -0500 (CDT) From: Niharendu.Choudhury~at~mail.uh.edu Subject: hbuild for protein PDB file To: chemistry~at~ccl.net Message-id: <482863779.1057356948114.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT Hi all, I downloaded the PDB file for BPTI from protein data bank. I would like to add hydrogens on to it and finally run the dynamics in CHARMM. Can anyone supply me a CHARMM input file for adding (building) Hydrogens to the PDB files of BPTI? Thanking you Nihar From chemistry-request@ccl.net Sat Jul 5 04:51:29 2003 Received: from antigen.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h658pSqe018037 for ; Sat, 5 Jul 2003 04:51:29 -0400 Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 19216; Sat, 05 Jul 2003 01:52:55 -0700 (PDT) Received: from antigen.scripps.edu (elvis [137.131.130.25]) by relay2.scripps.edu (8.11.7/TSRI-4.4.1r) with SMTP id h658pR812011 for ; Sat, 5 Jul 2003 01:51:27 -0700 (PDT) Received: from elvis.scripps.edu(137.131.130.25) by antigen.scripps.edu via csmap id 19212; Sat, 05 Jul 2003 01:52:54 -0700 (PDT) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id BAA388728 for ; Sat, 5 Jul 2003 01:51:27 -0700 (PDT) Date: Sat, 5 Jul 2003 01:51:27 -0700 (PDT) From: Maneesh Yadav X-Sender: yadavm@elvis To: chemistry~at~ccl.net Subject: Molecular Surface Diversity Measure (of a cavity) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, As far as I can tell, there hasn't seemed to have been (any need for?) a diversity measure of protein host surfaces...but please let me know if I am wrong. Does anyone know of an example of a molecular diversity measure, based on molecular surfaces, being applied to an "anti-molecule" (i.e. the surface of a binding site on a protein)? Or if not an example, at least a method that might be sensible to give a try... I shy away from simply applying a diversity measure to the binding domain, as I would actually like to compare sites which are in very different places on different proteins... Many Thanks, Maneesh From chemistry-request@ccl.net Fri Jul 4 18:24:22 2003 Received: from mail.uh.edu (SanJacinto.Mail.UH.EDU [129.7.69.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h64MOMqe008692 for ; Fri, 4 Jul 2003 18:24:22 -0400 Received: from conversion-daemon by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0HHI00501U8GYF{at}mail.uh.edu> for chemistry{at}ccl.net; Fri, 4 Jul 2003 17:24:16 -0500 (CDT) Received: from localhost (Colorado.Mail.UH.EDU [129.7.69.103]) by mail.uh.edu (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0HHI00590U8G8L{at}mail.uh.edu>; Fri, 04 Jul 2003 17:24:16 -0500 (CDT) Date: Fri, 04 Jul 2003 17:24:16 -0500 (CDT) From: Niharendu.Choudhury{at}mail.uh.edu Subject: Re: CCL:Ewald in CHARMM To: Rick Venable Cc: chemistry{at}ccl.net Message-id: <482769665.1057357456126.JavaMail.root@localhost> MIME-version: 1.0 X-Mailer: Sun(TM) Web Access 1.2 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7BIT Hi all, I was initially running with following crystal keywords: Crystal Define Cubic 24.850 24.850 24.850 90.0 90.0 90.0 Crystal Build noperations 0 and energy keywords : ENERGY ATOM ELEC EWALD KAPPA 0.21 KMAX 4 KSQMAX 27 - CUTNB 10.0 CUTIM 10.0 CTOFNB 9.5 VDW SHIFT it was running fine. Now I have changed the energy section to the following: ENERGY ATOM ELEC EWALD KAPPA 0.21 KMAX 4 KSQMAX 27 - CUTNB 12.0 CUTIM 12.0 CTOFNB 10 VDW SHIFT and it is not running. (I have only changed cutnb and ctofnb, crystal section being the same). FOR MORE DETAILS I am appending below the output error message: -------------------------------------------------------------- CHARMM> ! energy parameters CHARMM> !energy - CHARMM> ! CUTNB 12.0 CUTIM 12.0 CTOFNB 10.0 VSWITCH SHIFT CDIE EP S 1 CHARMM> ! ATOM ELEC EWALD KAPPA 0.21 KMAX 4 KSQMAX 27 ORDER 6 - CHARMM> energy cutnb 12.0 cutim 12.0 ctonnb 7.5 ctofnb 9.0 - CHARMM> vswitch shift cdie eps 1 : updating the image atom lists and remapping Transformation Atoms Groups Residues Min-Distance 1 C001 has 66 22 22 0.00 2 C002 has 264 88 88 0.00 3 C003 has 60 20 20 0.00 4 C004 has 312 104 104 0.00 5 C005 has 765 255 255 0.00 6 C006 has 225 75 75 0.00 7 C007 has 303 101 101 0.00 8 C008 has 777 259 259 0.00 9 C009 has 255 85 85 0.00 10 C010 has 744 248 248 0.00 12 C012 has 66 22 22 0.00 13 C013 has 309 103 103 0.00 14 C014 has 87 29 29 0.00 Total of 5769 atoms and 1923 groups and 1923 residues were included NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 12.000 CTEXNB =999.000 CTONNB = 7.500 CTOFNB = 9.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 1536 exclusions and 0 interactions(1-4) found 0 group exclusions. found 0 image group exclusions. Generating nonbond list with Exclusion mode = 5 SPACE FOR 277948 ATOM PAIRS AND 0 GROUP PAIRS SPACE FOR 416942 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 300339 ATOM PAIRS WERE FOUND FOR ATOM LIST 17336 GROUP PAIRS REQUIRED ATOM SEARCHES ***** LEVEL -4 WARNING FROM ***** ***** CANNOT EXPAND HEAP ON THIS MACHINE ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5 Execution terminated due to the detection of a fatal error. ABNORMAL TERMINATION MAXIMUM STACK SPACE USED IS 76476 STACK CURRENTLY IN USE IS 76476 MOST SEVERE WARNING WAS AT LEVEL -4 HEAP PRINTOUT- HEAP SIZE 1024000 SPACE CURRENTLY IN USE IS 1348684 MAXIMUM SPACE USED IS 1348684 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 530624 NEXT: 970561 -------------------------------------------------------------------------- End of out put. If you kindly help me. Nihar From chemistry-request@ccl.net Sun Jul 6 14:00:58 2003 Received: from mail.szote.u-szeged.hu (mail.szote.u-szeged.hu [160.114.96.63]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h66I0qqe030037 for ; Sun, 6 Jul 2003 14:00:57 -0400 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr{at}ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id UAA23017 for ; Sun, 6 Jul 2003 20:00:49 +0200 Received: (qmail 8439 invoked by uid 525); 6 Jul 2003 18:00:49 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 6 Jul 2003 18:00:49 -0000 Date: Sun, 6 Jul 2003 20:00:49 +0200 (CEST) From: "Dr. Csaba Hetenyi" To: Dominique Vlieghe cc: forum CCL Subject: Re: CCL:AutoDock and protein-protein interactions In-Reply-To: <1057306539.12980.2.camel{at}dmbr032.fvms.ugent.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Protein-peptide interactions were investigated in the following paper. In one case, the peptide was "cut" from an other protein, mimicking its loop. --- Hetenyi and van der Spoel, Protein Sci. 2002 11(7) 1729-1737. --- Large peptides may cause trouble for the search engine, that is larger ones with more than 15 free torsions... Best wishes, Csaba On 4 Jul 2003, Dominique Vlieghe wrote: > Hello all, > > > * A general question: > I was wondering whether AutoDock is suitable for studying > protein-protein interactions. In principle it is, but speed is the > practical limitation I presume. Does anyone have experience with this? From chemistry-request@ccl.net Sat Jul 5 15:06:57 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h65J6uqe026585 for ; Sat, 5 Jul 2003 15:06:57 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 19YsN6-0005UW-NL for chemistry$at$ccl.net; Sat, 05 Jul 2003 20:06:56 +0100 Received: from matpc18.mats.qmw.ac.uk ([138.37.43.64] helo=Ruzhen) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 19YsN5-00016j-00 for chemistry$at$ccl.net; Sat, 05 Jul 2003 20:06:55 +0100 Message-ID: <004501c34328$600ddd20$402b258a@Ruzhen> From: "Ru-Zhen Li" To: Subject: how to build crystal structure using tinker? Date: Sat, 5 Jul 2003 20:05:18 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.64 Dear all, I am trying to build the beta-cristobalite structure using the crysal subroutine in the Tinker package, but it seems that it needs some Cartesian coordinates file type as input file, I am little bit confused, what kind of input file should it be? I mean in what format? has anyone have experience in this? can anyone give me some details? Thank you!! Ru-Zhen