From chemistry-request@ccl.net Fri Nov 7 00:47:56 2003 Received: from front3.chartermi.net (front3.chartermi.net [24.213.60.109]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA75lOVc027912 for ; Fri, 7 Nov 2003 00:47:24 -0500 Received: from [24.236.135.230] (HELO mmserver) by front3.chartermi.net (CommuniGate Pro SMTP 4.0.6) with SMTP id 418941816; Fri, 07 Nov 2003 00:47:24 -0500 Message-ID: <000701c3a4f2$9c55dea0$0901a8c0@mmserver> From: "Jim Kress" To: "Dmitry Rozmanov" , "CCL" References: <3FAAC611.2030100|at|xenon.spb.ru> Subject: Re: CCL:good molecular builder Date: Fri, 7 Nov 2003 00:47:20 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" 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-Spam-Status: No, hits=-1.0 required=7.0 tests=QUOTED_EMAIL_TEXT,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Try ArgusLab http://www.arguslab.com/ Jim ----- Original Message ----- From: "Dmitry Rozmanov" To: "CCL" Sent: Thursday, November 06, 2003 5:07 PM Subject: CCL:good molecular builder > Hello. > > Could anyone suggest a convenient molecular builder. My task is, say, I > have optimized geometry for water and nitric anion. Then I want to > compose a system using their geometries with cation, anion and 10 waters. > > It is enough if it saves xyz file. In fact it is preferably. > > Any suggestions? Everything I saw either shows molecules or offer > building but from the very scratch. > > Thank you all in advance. > > Regards. > > ---Dmitry. > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl|at|ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Fri Nov 7 08:59:40 2003 Received: from usstp09.itcs.purdue.edu (usstp09.itcs.purdue.edu [128.210.5.248]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7Dx8Vc011223 for ; Fri, 7 Nov 2003 08:59:08 -0500 Received: from bfp.cc.purdue.edu (bfp.cc.purdue.edu [128.210.189.30]) by usstp09.itcs.purdue.edu (8.12.10/8.12.10/scan-smtp) with ESMTP id hA7Dx8A1008248; Fri, 7 Nov 2003 08:59:08 -0500 Date: Fri, 7 Nov 2003 08:59:08 -0500 (EST) From: Bryan Putnam X-X-Sender: bfp:at:bfp.cc.purdue.edu To: "Close, David M." cc: chemistry:at:ccl.net Subject: Re: CCL:Dual Xeon & G98 In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new on Purdue Mailhub X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Tue, 4 Nov 2003, Close, David M. wrote: > CCL'ers: > Someone told me I can run G98 jobs faster on my Dell 530 Workstation > if IX use %Nproc=2 and make the following changes to the LINUX kernel > for sharing memory. > > echo "67108864" >/proc/sys/kernel/shmmax > echo "67108864" >/proc/sys/kernel/shmall > > only replace 67108864 with the amount of memory in your machine (in bytes) > Also, I know that the %Mem= should be per processor. Therefore, since I > have 512Mb total memory and 2 processors, I should use something like > %Mem=230Mb > Having done all this and also checking that the SMP kernel was running, > I cannot get this to work. After only a second the program quits where > the list of links to be used is printed. The program ends with an > "shmget failed" statement. I presume this has something to do with > shared memory, but I am not sure what to try next. Perhaps someone > knows what to try next, or perhaps what diagnostics to use to make sure > the system has been configured properly. > Regards, Dave Close. > > > Here are some notes I received on this... -Bryan IF YOU WANT TO RUN SHARED-MEMORY ON AN SMP system. Linux assumes that you want to share only small portions of memory, where Gaussian wants big chunks. To allow larger chunks of memory to be shared, add the following lines to /etc/sysctl.conf (requires reboot as this forces a re-configure of the kernel at boot): kernel.shmmax=134217728 kernel.shmall=134217728 (134217728 = 128*1024*1024 = 128Mb) You may set this according to your memory needs. You are supposed to be able to write to the /proc/sys/kernel files that control this on-the-fly, but it didn't seem to work for me and would have to be done after each reboot anyway. From chemistry-request@ccl.net Fri Nov 7 07:57:09 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7CubVc009000 for ; Fri, 7 Nov 2003 07:56:38 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HNZ00B6GFYE03/at/mailserver.unimi.it> for chemistry/at/ccl.net; Fri, 07 Nov 2003 13:56:39 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HNZ00614FYBM5/at/smtp.unimi.it> for chemistry/at/ccl.net; Fri, 07 Nov 2003 13:56:35 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 7FD0410458; Fri, 07 Nov 2003 14:08:41 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 517BE10045; Fri, 07 Nov 2003 14:08:41 +0100 (CET) Date: Fri, 07 Nov 2003 14:08:40 +0100 (CET) From: Alessandro Contini Subject: re:CCL:summary mp2/cc-pvtz In-reply-to: <200311071003.LAA27638/at/web1.ulb.ac.be> To: Giju Kalathingal Cc: chemistry/at/ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 References: <200311071003.LAA27638/at/web1.ulb.ac.be> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hA7Cv9Vc009008 Hi, thanks for your reply. I was trying to perform some nmr calculations with mp2 and triple split valence basis; I tried it also with the maxdisk key and the calc crashes; however the value that is reported at the end of the output file is really huge (about 280GB) and I don't have that much scratch available. I'll try anyway as you suggest to put the reported value as maxdisk, but I'm afraid to overflow our cluster (used by a certain number of people!). I'll let you know Thanks again Alessandro On Fri, 7 Nov 2003, Giju Kalathingal wrote: > Hello, > Since I had missed your query to CCL, could you please > send me your question again? > I don't know what others replied to you. However, > you may try to use "maxdisk" (for, e.g., 50GB), first > with specifying some lower amount of memory. If the > calc crashes, the output will give you some info. > Then redo by specifying that amount of memory. > It worked for me in the past. > > Sincerely, > Giju Kalathingal > > PS. Let me know the outcome. > > >Hi, > >I'd like to thanks Marcel Swart, Stephen Garrison, Olga Dmitrenko and > >Giovanni Scalmani for the kind reply. > >The problem as suggested was derived by a "out of disk" or "out of memory" > >error (the famous -1); however I could not solve it because the disk > >requested for my system was 280GB and more for a semidirect and at least > >25GB of memory for a direct optimization. However the calculation run > >properly with B3LYP/cc-pvtz, B3LYP/tzvp and B3LYP/6-311+G(2d,p) basis. > > > >Thanks again > > > >Alessandro Contini > > > >Alessandro Contini, Ph.D. > >Istituto di Chimica Organica "Alessandro Marchesini" > >Universit` degli Studi di Milano, Facolt` di Farmacia > >Via Venezian, 21 20133 Milano > >Tel. +390250314480 Fax. +390250314476 > >e-mail alessandro.contini/at/unimi.it > > > > > > > > > >-= This is automatically added to each message by the mailing script =- > >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > >and send your message to: CHEMISTRY/at/ccl.net > > > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net > >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > >If your mail is bouncing from CCL.NET domain send it to the maintainer: > >Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) > >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > > > > > > Dear , > > With best regards, > Giju Kalathingal > > Present Address:- > Dr. Kalathingal Thomas Giju > Department of General Chemistry (ALGC) > Vrije Universiteit Brussel > Pleinlaan 2, 1050 Brussels, Belgium. > Tel.:++32-2-629-3315 Fax: ++32-2-629-3317 > E-mail: Giju.Kalathingal/at/vub.ac.be > > > Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini/at/unimi.it From chemistry-request@ccl.net Fri Nov 7 10:35:02 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7FYVVc013994 for ; Fri, 7 Nov 2003 10:34:31 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1AI8bl-00006f-U9 for chemistry/at/ccl.net; Fri, 07 Nov 2003 11:33:09 -0400 Received: from 138.73.24.161 ( [138.73.24.161]) as user kgdct/at/mailserv.mta.ca by webmail.mta.ca with HTTP; Fri, 7 Nov 2003 11:33:09 -0400 Message-ID: <1068219189.3fabbb35dd468/at/webmail.mta.ca> Date: Fri, 7 Nov 2003 11:33:09 -0400 From: Katie Doucet To: CCL Subject: partial atomic charges, fragmental volume and solvation parameters in AUTODOCK3 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I was wondering if there was a program, as well as intructions how, to add partial atomic charges, fragmental volume and solvation parameters to a pdb file to create a pdbqs file for use in AUTODOCK3 on a LINUX machine. Thanks K. Doucet From chemistry-request@ccl.net Fri Nov 7 10:31:21 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7FUoVc013850 for ; Fri, 7 Nov 2003 10:30:50 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1AI8YC-0008Vf-AG for chemistry/at/ccl.net; Fri, 07 Nov 2003 11:29:28 -0400 Received: from 138.73.24.161 ( [138.73.24.161]) as user kgdct/at/mailserv.mta.ca by webmail.mta.ca with HTTP; Fri, 7 Nov 2003 11:29:28 -0400 Message-ID: <1068218968.3fabba5845e95/at/webmail.mta.ca> Date: Fri, 7 Nov 2003 11:29:28 -0400 From: Katie Doucet To: CCL Subject: Sybyl for LINUX MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I was wondering if there was such a thing a Sybyl for LINUX fo the prupose of adding partial atomic charges to a pdb file? If so how does one go about gettting it? thanks K.Doucet From chemistry-request@ccl.net Fri Nov 7 03:59:37 2003 Received: from mailshell.com (web01.mailshell.com [209.157.66.231]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hA78x5Vc001225 for ; Fri, 7 Nov 2003 03:59:06 -0500 Received: (qmail 20126 invoked by uid 99); 7 Nov 2003 08:59:05 -0000 Message-ID: <1068195545.3fab5ed9afc90/at/www.mailshell.com> Date: Fri, 07 Nov 2003 00:59:05 -0800 X-Priority: 3 (Normal) From: To: chemistry/at/ccl.net Subject: volume and surface of fragment In-Reply-To: <000701c3a4f2$9c55dea0$0901a8c0@mmserver> MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit User-Agent: Mailshell.com X-Spam-Status: No, hits=0.8 required=7.0 tests=IN_REP_TO,NO_REAL_NAME,PRIORITY_NO_NAME,USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I need to calculate volumes and surfaces of molecular fragments that fall within a given sphere (i.e. for the space falling within the union of the big sphrere and the van der Waals volume of the molecule intersected by it). Is there any simple way to do it (preferably under Windoze)? Thanks - Zoli _______________________________________________________ The FREE service that prevents junk email http://www.mailshell.com From chemistry-request@ccl.net Fri Nov 7 08:23:31 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7DMvVc009953 for ; Fri, 7 Nov 2003 08:22:59 -0500 Received: from chem.vu.nl ([130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AI5kI-000NGmC; Fri, 7 Nov 2003 13:29 +0100 Message-ID: <3FAA7D77.3050803^at^chem.vu.nl> Date: Thu, 06 Nov 2003 17:57:27 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Ru-Zhen,Li" CC: "CHEMISTRY^at^ccl.net" Subject: Re: CCL:build amyloid peptide by hand--problem in peptide bond!!! References: In-Reply-To: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.9 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,PLING_PLING,QUOTED_EMAIL_TEXT, REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Ru-Zhen,Li wrote: > Dear all, > > > I was trying to build a amyloid peptide with the builder module in Insight2, the sequence is > DAEFR---HDSGY---EVHHQ---KLVFF---AEDVG---SNKGA---IIGLM---VGGVV---IAT > > What I am confused is: as we all know, there are two hydrogens on the amino group, and if I choose different hydrogen to form the peptide bond with the carboxylic acid group from the previous amino acids, I will have different structure, one is quite global, and another is quite linear. > > what I really what to know is, since the amino acids is not symmetrical, the two hydrogens must be different to construct the secondary structure, shall I just select the two hydrogens randomly or shall I select a particular hydrogen? the peptide might choose the structure which has the lowest energy, but the problem is, since there are so many amino acids, there will be too many possibilities, how can I know which one is right? > > can anyone tell me what is the truth in real protein? This is the famous 'protein folding problem', meaning you cannot know or predict this straightaway. If you have e.g. NMR measurements, or X-ray structure, you're done ofcourse. You could search the PDB for homologous sequences and try the corresponding structures. Otherwise, try a long (>>100ns!) M simulation and see whether significantly populated clusters develop. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra^at^chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Fri Nov 7 07:30:20 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7CTmVc008578 for ; Fri, 7 Nov 2003 07:29:48 -0500 Received: from chem.vu.nl ([130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AI5kH-000NGQC; Fri, 7 Nov 2003 13:29 +0100 Message-ID: <3FAA7BF1.1080301)at(chem.vu.nl> Date: Thu, 06 Nov 2003 17:50:57 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Joey Harriman CC: CCL posting Subject: Re: CCL:clustering database molecules References: <1068131652.3faa6544c4f16)at(webmail.unb.ca> In-Reply-To: <1068131652.3faa6544c4f16)at(webmail.unb.ca> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Joey Harriman wrote: > Hi, > > I am trying to cluster a database of a tetrapeptide with different geometries. I am > currently using MOE and have tried varying fingerprints (at the 99%) threshold with no > success. Does anyone have a good system for clustering different geometries of the > same molecule from a database? Thanks in advance for any help you can offer. There is a tool in the Gromacs (free under GPL at www.gromacs.org) package desinged to cluster conformations from an MD trajectory. It will accept concatenated .pdb files (all of the same molecule) as if it was a trajectory. It is called g_cluster and has several algorithms to cluster conformations\ based on their RMSD, or you can read an externally generated 'difference' matrix for your conformations. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra)at(chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Fri Nov 7 11:31:05 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7GUXVc016331 for ; Fri, 7 Nov 2003 11:30:33 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id hA7GUWqY027610 for ; Fri, 7 Nov 2003 17:30:32 +0100 (CET) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id hA7GUWAr331832; Fri, 7 Nov 2003 17:30:32 +0100 (MET) Date: Fri, 7 Nov 2003 17:30:32 +0100 (MET) From: Michel Petitjean Message-Id: <200311071630.hA7GUWAr331832/at/ds10.itodys.jussieu.fr> To: chemistry/at/ccl.net Subject: CCL: Re:volume and surface of fragment X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=-0.5 required=7.0 tests=QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) To: chemistry/at/ccl.net Subj: CCL: Re:volume and surface of fragment (1) compute the volume of the big sphere V1 (2) compute the van der Waals volume V2 (3) compute the volume of the union V3 The intersection between the big sphere and the van der Waals volume has for volume V = V1 + V2 - V3, because the volume of the union is V3 = V1 + V2 - V. The freeware ASV is able to compute all these volumes: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Sorry, no Windows Version. Michel Petitjean, Email: petitjean/at/itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean/at/ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html >From: > >I need to calculate volumes and surfaces of molecular fragments > that fall within a given sphere (i.e. for the space falling > within the union of the big sphrere and the van der Waals volume > of the molecule intersected by it). Is there any simple way to do it > (preferably under Windoze)? > > Thanks - Zoli From chemistry-request@ccl.net Fri Nov 7 11:20:48 2003 Received: from youkai.llnl.gov (youkai.llnl.gov [134.9.187.176]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7GKGVc015757 for ; Fri, 7 Nov 2003 11:20:17 -0500 Received: from youkai.llnl.gov (localhost.localdomain [127.0.0.1]) by youkai.llnl.gov (8.12.8/8.12.5) with ESMTP id hA7GKG8o016232; Fri, 7 Nov 2003 08:20:16 -0800 Received: from localhost (brian@localhost) by youkai.llnl.gov (8.12.8/8.12.5/Submit) with ESMTP id hA7GKG9Z016228; Fri, 7 Nov 2003 08:20:16 -0800 Date: Fri, 7 Nov 2003 08:20:16 -0800 (PST) From: Brian Bennion To: Katie Doucet cc: CCL Subject: Re: CCL:partial atomic charges, fragmental volume and solvation parameters in AUTODOCK3 In-Reply-To: <1068219189.3fabbb35dd468_at_webmail.mta.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.2 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,SIGNATURE_LONG_DENSE, USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, There are scripts included with the autodock3 distribution that can help you accomplish your jobs. q.amber for charges and others. Look at the online documentation from the autodock website Brian On Fri, 7 Nov 2003, Katie Doucet wrote: > > > I was wondering if there was a program, as well as intructions how, to add > partial atomic charges, fragmental volume and solvation parameters to a pdb > file to create a pdbqs file for use in AUTODOCK3 on a LINUX machine. > > Thanks > K. Doucet > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl_at_ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 422-6605 ** ***************************************************************** From chemistry-request@ccl.net Fri Nov 7 13:04:07 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7I3aVc019562 for ; Fri, 7 Nov 2003 13:03:36 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id hA7I3WdP032602 for ; Fri, 7 Nov 2003 14:03:32 -0400 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id hA7I3VjS009524 for ; Fri, 7 Nov 2003 14:03:31 -0400 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id hA7I3Vc1009505 for chemistry_at_ccl.net; Fri, 7 Nov 2003 14:03:31 -0400 Received: from raven.chem.unb.ca (raven.chem.unb.ca [131.202.164.46]) by webmail.unb.ca (IMP) with HTTP for ; Fri, 7 Nov 2003 14:03:31 -0400 Message-ID: <1068228211.3fabde73311f1_at_webmail.unb.ca> Date: Fri, 7 Nov 2003 14:03:31 -0400 From: "Flight, Robert Maxwell" Reply-to: robert.flight_at_unb.ca To: Computational Chemistry List Subject: Re: CCL:partial atomic charges, fragmental volume and solvation parameters in AUTODOCK3 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.164.46 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-1.1, required 5, FROM_HAS_MIXED_NUMS, QUOTED_EMAIL_TEXT, SPAM_PHRASE_00_01, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-0.8 required=7.0 tests=QUOTED_EMAIL_TEXT,USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Katie, > I was wondering if there was a program, as well as intructions how, to add > partial atomic charges, fragmental volume and solvation parameters to a pdb > file to create a pdbqs file for use in AUTODOCK3 on a LINUX machine. Try AutoDockTools, it runs on Windows, Unix and LINUX, there is a link from the main AutoDock site (http://www.scripps.edu/pub/olson-web/doc/autodock/index.html), and there are plenty of examples as well. -Robert *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight_at_unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy ----- End forwarded message ----- *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight_at_unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy From chemistry-request@ccl.net Fri Nov 7 15:33:44 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7KXDVc023597 for ; Fri, 7 Nov 2003 15:33:13 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1AIDGp-0002h3-RQ for chemistry|at|ccl.net; Fri, 07 Nov 2003 16:31:51 -0400 Received: from 138.73.24.42 ( [138.73.24.42]) as user srwhttl|at|mailserv.mta.ca by webmail.mta.ca with HTTP; Fri, 7 Nov 2003 16:31:51 -0400 Message-ID: <1068237111.3fac0137c9bea|at|webmail.mta.ca> Date: Fri, 7 Nov 2003 16:31:51 -0400 From: srwhttl|at|mta.ca To: chemistry|at|ccl.net Subject: ONIOM calculation (with AMBER): "Missing atomic parameters" MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.42 X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi everyone, I am trying to run an ONIOM calculation with B3LYP/6-31+G(d,p) as a high layer and Amber as my low layer. The error at the end of the file says I am missing atomic parameters (see below for the last part of the calc file). What are these atomic parameters and where would I obtain them to get my calculation to work? Thanking You in Advance, Sarah Whittleton Mount Allison University Th calcaultion dies almost immediatley and ends with: I= 105 IAn= 15 Valence= 4. JB= 1 J= 106 IAn= 8 IBT= 1 Dist= 1.80D+00 JB= 2 J= 107 IAn= 8 IBT= 2 Dist= 1.48D+00 JB= 3 J= 171 IAn= 8 IBT= 1 Dist= 1.80D+00 JB= 4 J= 104 IAn= 8 IBT= 2 Dist= 1.58D+00 Missing atomic parameters for atom 207 IAtTyp= 20000000 Missing atomic parameters. Error termination via Lnk1e in /var/local/g03/l101.exe at Fri Nov 7 15:18:04 2003. Job cpu time: 0 days 0 hours 0 minutes 0.6 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1 From chemistry-request@ccl.net Fri Nov 7 15:35:07 2003 Received: from Princeton.EDU (postoffice01.Princeton.EDU [128.112.129.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7KYaVc023662 for ; Fri, 7 Nov 2003 15:34:36 -0500 Received: from smtpserver2.Princeton.EDU (smtpserver2.Princeton.EDU [128.112.129.148]) by Princeton.EDU (8.12.9/8.12.9) with ESMTP id hA7KYa3f018146 for ; Fri, 7 Nov 2003 15:34:36 -0500 (EST) Received: from Princeton.EDU (lotus.Princeton.EDU [128.112.81.82]) (authenticated bits=0) by smtpserver2.Princeton.EDU (8.12.9/8.12.9) with ESMTP id hA7KYZma008139 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Fri, 7 Nov 2003 15:34:35 -0500 (EST) Message-ID: <3FAC01DB.7090703|at|Princeton.EDU> Date: Fri, 07 Nov 2003 15:34:35 -0500 From: Silviu Zilberman User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6a) Gecko/20031029 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry|at|ccl.net Subject: molecular viewers questions Content-Type: multipart/alternative; boundary="------------070309010109020008090501" X-Spam-Status: No, hits=1.2 required=7.0 tests=HTML_20_30,HTML_MESSAGE,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --------------070309010109020008090501 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi, I have electronic density data for various systems. In gOpenMol, one can easily plot iso-density contours. However, I did not find a way to plot the iso-density surface containing a given amount (say 90%) of the *total* charge density. Do you know weather it can be done with gOpenMol, or any other viewer? Thanks, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu, PhD Post doctoral research associate 213 Frick Laboratory, Department of Chemistry Princeton University Princeton, NJ 08544 phone: 609-258-1834 fax: 609-258-6746 silviu|at|Princeton.EDU Yahoo! Messenger ID: silviu_zilberman %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --------------070309010109020008090501 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi,

I have electronic density data for various systems. In gOpenMol, one can easily plot iso-density contours. However, I did not find a way to plot the iso-density surface containing a given amount (say 90%) of the total charge density.

Do you know weather it can be done with gOpenMol, or any other viewer?

Thanks, Silviu.
-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Zilberman Silviu, PhD
Post doctoral research associate
 
213 Frick Laboratory, Department of Chemistry 
Princeton University
Princeton, NJ 08544
 
phone: 609-258-1834
fax:   609-258-6746
silviu|at|Princeton.EDU
Yahoo! Messenger ID: silviu_zilberman
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--------------070309010109020008090501-- From chemistry-request@ccl.net Fri Nov 7 16:29:44 2003 Received: from mailgate.tripos.com (mailgate.tripos.com [192.160.145.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA7LTDVc025149 for ; Fri, 7 Nov 2003 16:29:13 -0500 Message-ID: From: "Paul Hawkins" To: "Katie Doucet" , "CCL" Date: Fri, 7 Nov 2003 16:28:56 -0500 Subject: RE: Sybyl for LINUX MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4925.2800 In-Reply-To: <1068218968.3fabba5845e95.-at-.webmail.mta.ca> Importance: Normal X-Spam-Status: No, hits=-0.4 required=7.0 tests=IN_REP_TO,MSGID_GOOD_EXCHANGE,PRIORITY_NO_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Katie, In the 6.9.1 release of SYBYL (on Linux or IRIX) there is a command in the Biopolymer module "Load Charges". This allows you add charges from a variety of charge treatments for both the protein and any bound ligand/cofactors etc. Paul Hawkins Applications Scientist Tripos Inc 1699 South Hanley Road St. Louis MO 63144 Ph: 617-899-4151 E-mail: phawkins.-at-.tripos.com www.tripos.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On Behalf Of Katie Doucet Sent: Friday, November 07, 2003 10:29 AM To: CCL Subject: CCL:Sybyl for LINUX I was wondering if there was such a thing a Sybyl for LINUX fo the prupose of adding partial atomic charges to a pdb file? If so how does one go about gettting it? thanks K.Doucet -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY.-at-.ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+