From chemistry-request@ccl.net Tue Jun 29 08:53:24 2004 Received: from ms-dienst.rz.rwth-aachen.de (ms-1.rz.RWTH-Aachen.DE [134.130.3.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5TDrMAk016122 for ; Tue, 29 Jun 2004 08:53:23 -0500 Received: from r220-1 (r220-1.rz.RWTH-Aachen.DE [134.130.3.31]) by ms-dienst.rz.rwth-aachen.de (iPlanet Messaging Server 5.2 HotFix 1.12 (built Feb 13 2003)) with ESMTP id <0I0200EJXP8EXX|at|ms-dienst.rz.rwth-aachen.de> for chemistry|at|ccl.net; Tue, 29 Jun 2004 15:53:03 +0200 (MEST) Received: from relay.RWTH-Aachen.DE ([134.130.3.1]) by r220-1 (MailMonitor for SMTP v1.2.2 ) ; Tue, 29 Jun 2004 15:52:57 +0200 (MEST) Received: from post.rwth-aachen.de (ms-1.rz.RWTH-Aachen.DE [134.130.3.130]) by relay.rwth-aachen.de (8.12.10/8.12.7-1) with ESMTP id i5TDqtmH014700 for ; Tue, 29 Jun 2004 15:52:56 +0200 (MEST) Received: from [134.130.122.44] by ms-dienst.rz.rwth-aachen.de (mshttpd); Tue, 29 Jun 2004 15:52:55 +0200 Date: Tue, 29 Jun 2004 15:52:55 +0200 From: Mitja Medved Subject: periodic boundary conditions To: chemistry|at|ccl.net Message-id: <404793402e52.402e52404793|at|post.rwth-aachen.de> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.12 (built Feb 13 2003) Content-type: text/plain; charset=us-ascii Content-language: en Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: en Priority: normal X-Spam-Status: No, hits=4.9 required=7.5 tests=IMPRONONCABLE_1,MY_BAD_DOT, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello! Apart from other programs, we work with Gaussian'03 using GaussView as GUI. I tried to calculate the geometry of given molecule (aminoethanol) in explicit solvent (25 water molecules) placed randomly around the solute. The whole cluster should, of course, not be in vaccuum, so I intended to use periodic boundary conditions. However, it seems that this does not work for amorphous materials. Furthermore, when using PBC, it seems that one can not use ONIOM simultaneously. Do anyone have experience or suggestions, how this problem can be accomplished? Is this the right software to do this, anyway? I heard that DMol3 by Accelrys can do such miracles. In case it does: When energetics of the reaction (aminoethanol and water, base and acid in explicit solvent) should be found out, can one really rely on the energies given in output. In case of not using PBC the geometry of the whole constallation will change significantly, not only in the reaction centre. In case of PBC, what is the real energy that holds for one single cell? Thank you for halping me out of trouble! Regards, Mitja P.S.: This is my first posting, so I do not know how all this communication works. **************************************************** o/^ Dipl.-Ing. Mitja Medved medved|at|ivt.rwth-aachen.de Institut fuer Verfahrenstechnik RWTH Aachen University Turmstrasse 46, 52056 Aachen, Germany Phone: ++49(0)241-80-9-54-80 Telefax: ++49(0)241-80-9-22-52 www.ivt.rwth-aachen.de **************************************************** From chemistry-request@ccl.net Tue Jun 29 20:42:01 2004 Received: from um.edu.my ([202.185.111.180]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5U1ftbN018874 for ; Tue, 29 Jun 2004 20:41:59 -0500 Received: (qmail 25287 invoked by uid 99); 30 Jun 2004 09:47:06 +0800 Date: 30 Jun 2004 09:47:06 +0800 Message-ID: <20040630014706.25286.qmail/at/um.edu.my> To: Subject: autodock questions X-Mailer: UMMAIL 1.0 X-Originating-IP: 202.185.111.162 Content-Type: text/plain; charset=iso-8859-1 From: X-Spam-Status: No, hits=4.1 required=7.5 tests=NO_RDNS2,NO_REAL_NAME, RCVD_IN_RFCI autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I have been trying to compile the autotors portion of AutoDock with the command gcc -O3 -o autotors autotors.c as instructed in the manual for Linux compilation, and kept getting these errors: autotors.c: In function `main': autotors.c:2261: warning: return type of `main' is not `int' /tmp/ccQE5T7j.o: In function `main': /tmp/ccQE5T7j.o(.text+0xa03a): undefined reference to `cos' collect2: ld returned 1 exit status What does it mean? And how do I go about rectifying this? Regards, Juraina -------------------------- http://www.um.edu.my -------------------------- http://www.um.edu.my From chemistry-request@ccl.net Tue Jun 29 17:30:29 2004 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5TMURbN009251 for ; Tue, 29 Jun 2004 17:30:28 -0500 Received: from 128.200.204.158 (dhcp-204158.bio.uci.edu [128.200.204.158]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i5TMZV1o012498 for ; Tue, 29 Jun 2004 15:35:35 -0700 Resent-Date: Tue, 29 Jun 2004 15:35:31 -0700 Resent-Message-Id: <200406292235.i5TMZV1o012498/at/smtp2.es.uci.edu> Date: Tue, 29 Jun 2004 15:35:25 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <929798807.20040629153525/at/uci.edu> To: chemistry/at/ccl.net Subject: Re[2]: CCL:Re[2]: how to calculate proton dissociation energy in GAUSSIAN03 Resent-from: Qiang Lu MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Errol, Sorry, I made a mistake. One structure is HIS/CYS3-/ZN2+ and the other one is HIS/CYS3/ZN2+. The only difference is the three hydrogen which are dissociated from thiol groups. HIS contains imidazole group. The energy with CYS3- is -3517.614525 au and with CYS3 is -3516.510491 au. The energy is the sum of electronic and thermal Enthalpies. They have the same basis set. I will ask the professor about the triplet issue. -- Best regards, Qiang mailto:qiangl/at/uci.edu =================Original message text=============== 2004 June 29 hello, If by energy you mean just the total energy given at the end of a calculation(this is electronic energy plus internuclear repilsion), like -293.173976 or whatever, then generally the bigger the molecule the more negative this is (experiment with a few small molecules; bigger basis sets also give more negative energies). So Cys3 etc should have a more negative (lower, bigger only if you ignore the minus sign) energy than Cys etc. I can't really answer the spin question since I don't know exactly what rour structure looks like; I suggest you discuss it with one of the professors. But I don't think it should be triplet. Good luck. EL ==== Qiang Lu wrote: >Hi Errol, > > I did a optimization on both structure. The final results show that >CYS3-/ZN2+ has higher energy than CYS/ZN2+. That seems not reasonable. >I also tried CYS2-/CYS/ZN2+ and CYS-/CYS2/ZN2+, but their final structure >are no longer as good a tetrahedral structure as that in the crystal >structure. So I guess it might be due to the spin. There is a fourth >ligand HIS binds to ZN2+. Triplet spin caused by the Nitrogen in the >imidozole group could give a different result from that of singlet spin. >I find this in the reference J. Phys. Chem. B, vol. 103, No. 41, 1999. >But I don't know how to determine when it should be triplet and when it >should be singlet in the QM calculation other than using final energy. >Or in another way, I don't know how the whole structure become triplet state. > > > ==============End of original message text=========== From chemistry-request@ccl.net Wed Jun 30 02:42:15 2004 Received: from um.edu.my ([202.185.111.180]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5U7gCXZ004890 for ; Wed, 30 Jun 2004 02:42:14 -0500 Received: (qmail 30143 invoked by uid 99); 30 Jun 2004 15:47:24 +0800 Date: 30 Jun 2004 15:47:24 +0800 Message-ID: <20040630074724.30142.qmail^at^um.edu.my> To: Subject: autotors Q's X-Mailer: UMMAIL 1.0 X-Originating-IP: 202.185.111.162 Content-Type: text/plain; charset=iso-8859-1 From: X-Spam-Status: No, hits=4.1 required=7.5 tests=NO_RDNS2,NO_REAL_NAME, RCVD_IN_RFCI autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I am trying to assign torsions to my peptide using this command autotors -h -a -b -A [bnd file] [pdbq file] [output] and keep getting a segmentation fault error. I am running autodock on redhat 7.3 and have already set the stack size to be unlimited. What can be the problem? Any feedback is really appreciated. Juraina -------------------------- http://www.um.edu.my From chemistry-request@ccl.net Tue Jun 29 10:18:01 2004 Received: from rwcrmhc11.comcast.net (rwcrmhc11.comcast.net [204.127.198.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5TFI0Ak022059 for ; Tue, 29 Jun 2004 10:18:00 -0500 Received: from planaria (c-24-18-168-183.client.comcast.net[24.18.168.183]) by comcast.net (rwcrmhc11) with SMTP id <200406291523130130056ik9e>; Tue, 29 Jun 2004 15:23:13 +0000 Reply-To: From: "Mark Thompson" To: , Subject: RE: MOPAC charges in excited state Date: Tue, 29 Jun 2004 08:23:11 -0700 Message-ID: <000201c45dec$fd0fc270$0200a8c0@planaria> 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-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) In-Reply-To: <1088477825.40e0da814e215)at(www.mailshell.com> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Zoli, If you are interested in excited state charges, you can get ZINDO excited state charges with ArgusLab 4.0. It's free for single-user academics faculty and students. http://www.arguslab.com Mark *************************** Mark Thompson ArgusLab PO Box 55207 Seattle, WA 98155 FAX: 206.440.3305 mark)at(arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net]On Behalf Of ccl)at(fekete.mailshell.com Sent: Monday, June 28, 2004 7:57 PM To: CHEMISTRY)at(ccl.net Subject: CCL:MOPAC charges in excited state I'm trying to get atomic charges for excited states with MOPAC v6 - but the charges output always seem to be that of the ground state (and the ones when MULLIKEN keyword is given look total garbage, not even summing up to any integer value)! Is there any way to get them correctly with this program? -- Zoli Fekete _______________________________________________________ The FREE service that prevents junk email http://www.mailshell.com -= 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, jlabanow)at(nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Jun 29 02:45:22 2004 Received: from um.edu.my ([202.185.111.132]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5T7jJZY018945 for ; Tue, 29 Jun 2004 02:45:20 -0500 Received: (qmail 20941 invoked by uid 99); 29 Jun 2004 15:50:30 +0800 Date: 29 Jun 2004 15:50:30 +0800 Message-ID: <20040629075030.20940.qmail)at(um.edu.my> To: Subject: autodock questions X-Mailer: UMMAIL 1.0 X-Originating-IP: 202.185.111.162 Content-Type: text/plain; charset=iso-8859-1 From: X-Spam-Status: No, hits=4.1 required=7.5 tests=NO_RDNS2,NO_REAL_NAME, RCVD_IN_RFCI autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I have been trying to compile the autotors portion of AutoDock with the command gcc -O3 -o autotors autotors.c as instructed in the manual for Linux compilation, and kept getting these errors: autotors.c: In function `main': autotors.c:2261: warning: return type of `main' is not `int' /tmp/ccQE5T7j.o: In function `main': /tmp/ccQE5T7j.o(.text+0xa03a): undefined reference to `cos' collect2: ld returned 1 exit status What does it mean? Regards, Juraina -------------------------- http://www.um.edu.my From chemistry-request@ccl.net Wed Jun 30 04:58:52 2004 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5U9wmxO014323 for >ccl.net>; Wed, 30 Jun 2004 04:58:51 -0500 Received: from chemaxon.hu (chemaxon.hu [127.0.0.1]) by chemaxon.hu (8.12.8/8.12.8) with ESMTP id i5UA41Dx007984; Wed, 30 Jun 2004 12:04:01 +0200 Received: from localhost (szjuhos@localhost) by chemaxon.hu (8.12.8/8.12.8/Submit) with ESMTP id i5UA41m7007980; Wed, 30 Jun 2004 12:04:01 +0200 Date: Wed, 30 Jun 2004 12:04:01 +0200 (CEST) From: Szilveszter Juhos >chemaxon.hu> To: juraina<>um.edu.my cc: chemistry<>ccl.net Subject: CCL:autodock questions In-Reply-To: <20040629075030.20940.qmail<>um.edu.my> Message-ID: >chemaxon.hu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 29 Jun 2004 juraina<>um.edu.my wrote: > autotors.c: In function `main': > autotors.c:2261: warning: return type of `main' is not `int' This is only a warning (declare main as int to eliminate). > /tmp/ccQE5T7j.o(.text+0xa03a): undefined reference to `cos' > collect2: ld returned 1 exit status Add the math library: gcc -O3 -o autotors autotors.c -lm Cheers: Szilva From chemistry-request@ccl.net Wed Jun 30 08:37:38 2004 Received: from mx1.tripos.com (mx1.tripos.com [192.160.145.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5UDbbxO027111 for ; Wed, 30 Jun 2004 08:37:37 -0500 Message-ID: From: "John Begemann" To: Date: Wed, 30 Jun 2004 08:42:51 -0500 Subject: CCL:Workshop: Virtual Screening with FlexX, second call MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Thread-Index: AcReqCMgUIDjv07MSICj0dzKuaLm4g== X-eShield-AntiVirus: Passed X-eShield-AntiVirus-Message: Scanned by http://www.bluecoat.com/eShield X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net "Virtual Screening Workshop" August 18-20, 2004 Princeton, New Jersey, USA Second call, date is approaching fast. Note workshop is held right before the Fall ACS in Philadelphia! This event is an intense two-day workshop designed by scientific experts at BioSolveIT and Tripos to provide hands-on training to customers interested in effectively utilizing their FlexX suite of in-silico discovery tools. This training course is designed to uncover the benefits that the FlexX suite of virtual screening tools can bring to your molecular modeling and computational chemistry programs. Scientists from both companies will train participants of this docking workshop using the latest software releases. This course will provide a mixture of lectures, workshops and discussions. Space for this scientific training session is limited, so please register soon. For further details see: http://www.tripos.com/flexxworkshop/flexxworkshopagenda.html. Alternatively contact Tripos at (mailto:contact_us/at/tripos.com) or BioSolveIT at (mailto:workshop/at/biosolveit.de) From chemistry-request@ccl.net Wed Jun 30 07:06:30 2004 Received: from web15213.mail.bjs.yahoo.com (web15213.mail.cnb.yahoo.com [202.43.216.143]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5UC6QxO022107 for ; Wed, 30 Jun 2004 07:06:27 -0500 Message-ID: <20040630121137.47457.qmail)at(web15213.mail.bjs.yahoo.com> Received: from [202.201.245.108] by web15213.mail.cnb.yahoo.com via HTTP; Wed, 30 Jun 2004 20:11:37 CST Date: Wed, 30 Jun 2004 20:11:37 +0800 (CST) From: =?gb2312?q?yong=20guo?= Subject: consultation,thank very much! To: chemistry)at(ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-881639290-1088597497=:46143" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=6.0 required=7.5 tests=DATE_IN_PAST_12_24, DEAR_SOMETHING,HTML_20_30,HTML_MESSAGE,IMPRONONCABLE_1,MK_BAD_HTML_04, MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-881639290-1088597497=:46143 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit dear sir: firstly,thank for your help. the calculation in PCM model perhaps exceed the ability of my computer.I try the opt calculation in SCI-PCM model in the same method and basis in PCM model.however it failed. the error information is following: >WARNING! Serious error in surface integrals. >Nuclear flux = 214.99 Qnuc = 218.00 Error in int = 0.00 >It is probable that some of the solute is outside the cavity and/or >parts of the cavity surface cannot be reached from the origin. >Try more integration points or a different set of integration origins. > >Surface Problems in SciFoc >Error termination via Lnk1e in e:\g03w\l502.exe at Tue Jun 29 16:41:38 2004. >Job cpu time: 0 days 0 hours 3 minutes 30.0 seconds. >File lengths (MBytes): RWF= 46 Int= 0 D2E= 0 Chk= 1 Scr= > 1 > according the clue on the error infromation, i used "Integral(Grid=UltraFine)"key word to increase integration points , but it failed again.perhaps another clue on the error infromation:different set of integration origins can help us to solve the question. however the question is how to decide different set of integration origins ? may you give me some consuction? thank for your generous help,havea nice time! > > > your sincere :guoyong > 2004 6 30 --------------------------------- Do You Yahoo!? 100UWSJOd9;2;9;SC#?QE;"5gSJWTVz@)H]#! --0-881639290-1088597497=:46143 Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: 8bit
dear sir:
            firstly,thank for your help. the calculation in PCM model perhaps exceed the ability of my computer.I try the opt calculation in SCI-PCM
model in the same method and basis in PCM model.however it failed. the error information is following:
>WARNING!  Serious error in surface integrals.
>Nuclear flux =    214.99 Qnuc =   218.00 Error in int =     0.00
>It is probable that some of the solute is outside the cavity and/or
>parts of the cavity surface cannot be reached from the origin.
>Try more integration points or a different set of integration origins.

>
>Surface Problems in SciFoc
>Error termination via Lnk1e in e:\g03w\l502.exe at Tue Jun 29 16:41:38
2004.
>Job cpu time:  0 days  0 hours  3 minutes 30.0 seconds.
>File lengths (MBytes):  RWF=     46 Int=      0 D2E=      0 Chk=     1
Scr=
>     1
>
  according the clue on the error infromation, i used "Integral(Grid=UltraFine)"key word to increase integration points , but it failed again.perhaps another clue on the error infromation:different set of integration origins  can help us to solve the question. however the question is how to decide different set of integration origins ? may you give me some consuction?  thank for your generous help,havea nice time!
>
>
>                                                 your sincere :guoyong

>                                                            2004  6 30


Do You Yahoo!?
100UWSJOd9;2;9;SC#?QE;"5gSJWTVz@)H]#! --0-881639290-1088597497=:46143-- From chemistry-request@ccl.net Wed Jun 30 04:00:54 2004 Received: from relay5.tp1rc.edu.tw (relay5.tp1rc.edu.tw [163.28.16.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5U90qxO010178 for ; Wed, 30 Jun 2004 04:00:53 -0500 Received: from ntu.edu.tw (chem135.ch.ntu.edu.tw [140.112.54.135]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by relay5.tp1rc.edu.tw (Postfix) with ESMTP id 486C6106DA0 for ; Wed, 30 Jun 2004 17:06:07 +0800 (CST) Message-ID: <40E2827D.5020606=at=ntu.edu.tw> Date: Wed, 30 Jun 2004 17:06:05 +0800 From: "Jerry C. C. Chan" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry=at=ccl.net Subject: molecular docking softwares Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CLLers, could anyone please tell me what MD packages (free or less than US$300) can deal with the interaction/docking between a molecule and a mineral surface (solvation model incorporated)? Can Tinker do the job? Thanks, Jerry -- Jerry C. C. Chan Tel: 886-02-23630231 Ext 2782 Chemistry Department Fax: 886-02-23636359 National Taiwan University No.1, Sec. 4, Roosevelt Road Taipei, Taiwan From chemistry-request@ccl.net Wed Jun 30 14:54:07 2004 Received: from mxout1.netvision.net.il (mxout1.netvision.net.il [194.90.9.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5UJs6W2025395 for ; Wed, 30 Jun 2004 14:54:06 -0500 Received: from fedor ([217.132.74.191]) by mxout1.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTPA id <0I0500AN80UO6Y[at]mxout1.netvision.net.il> for CHEMISTRY[at]ccl.net; Wed, 30 Jun 2004 22:59:13 +0300 (IDT) Date: Wed, 30 Jun 2004 23:26:32 +0200 From: Michael Subject: CCL: software to convert XYZ format to PDB ? To: CHEMISTRY[at]ccl.net Message-id: <003701c45ee8$ebad6710$b400a8c0@fedor> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Mailer: Microsoft Outlook Express 6.00.2800.1409 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=6.6 required=7.5 tests=LINES_OF_YELLING,NO_RDNS2, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I need to convert protein structure presented as XYZ (Cartesian coordinate file) to the PDB file format. The problem is that many software packages can do the job but not completely. In other words, when such software reads an XYZ file (see the fragment below): N -1.21000 43.30600 -19.48400 C -1.45100 43.83100 -20.83200 C -1.89300 45.28700 -20.70900 O -1.42200 46.16400 -21.43800 it generates the following PDB analog with unknown residual names and numbers: ATOM 462 N UNK A 1 -1.210 43.306 -19.484 1.00 0.00 ATOM 463 C UNK A 1 -1.451 43.831 -20.832 1.00 0.00 ATOM 464 C UNK A 1 -1.893 45.287 -20.709 1.00 0.00 ATOM 465 O UNK A 1 -1.422 46.164 -21.438 1.00 0.00 while the correct pdb file must specify the residual names and numbers: ATOM 462 N VAL 32 -1.210 43.306 -19.484 1.00 14.04 N ATOM 463 CA VAL 32 -1.451 43.831 -20.832 1.00 6.48 C ATOM 464 C VAL 32 -1.893 45.287 -20.709 1.00 8.17 C ATOM 465 O VAL 32 -1.422 46.164 -21.438 1.00 10.91 O I would highly appreciate if somebody can point me to the reliable free software for Windows. Kind regards, Michael From chemistry-request@ccl.net Wed Jun 30 13:38:53 2004 Received: from mxout4.netvision.net.il (mxout4.netvision.net.il [194.90.9.27]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5UIcqW2019697 for ; Wed, 30 Jun 2004 13:38:52 -0500 Received: from fedor ([217.132.74.191]) by mxout4.netvision.net.il (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTPA id <0I0400A1IXDIFB(at)mxout4.netvision.net.il> for CHEMISTRY(at)ccl.net; Wed, 30 Jun 2004 21:44:06 +0300 (IDT) Date: Wed, 30 Jun 2004 22:11:28 +0200 From: Michael Subject: CCL software to convert XYZ format to PDB ? To: CHEMISTRY(at)ccl.net Message-id: <000b01c45ede$6d804510$b400a8c0@fedor> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Mailer: Microsoft Outlook Express 6.00.2800.1409 Content-type: text/plain; charset=koi8-r Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=5.6 required=7.5 tests=NO_RDNS2,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I need to convert protein structure presented as XYZ (Cartesian coordinate file) to the PDB file format. The problem is that many software packages can do the job but not completely. In other words, when such software reads an XYZ file (see the fragment below): N -1.21000 43.30600 -19.48400 C -1.45100 43.83100 -20.83200 C -1.89300 45.28700 -20.70900 O -1.42200 46.16400 -21.43800 it generates the following PDB analog with unknown residual names and numbers: ATOM 462 N UNK A 1 -1.210 43.306 -19.484 1.00 0.00 ATOM 463 C UNK A 1 -1.451 43.831 -20.832 1.00 0.00 ATOM 464 C UNK A 1 -1.893 45.287 -20.709 1.00 0.00 ATOM 465 O UNK A 1 -1.422 46.164 -21.438 1.00 0.00 while the correct pdb file must specify the residual names and numbers: ATOM 462 N VAL 32 -1.210 43.306 -19.484 1.00 14.04 N ATOM 463 CA VAL 32 -1.451 43.831 -20.832 1.00 6.48 C ATOM 464 C VAL 32 -1.893 45.287 -20.709 1.00 8.17 C ATOM 465 O VAL 32 -1.422 46.164 -21.438 1.00 10.91 O I would highly appreciate if somebody can point me to the reliable free software for Windows. Kind regards, Michael From chemistry-request@ccl.net Wed Jun 30 17:29:49 2004 Received: from mhub-c3.tc.umn.edu (mhub-c3.tc.umn.edu [160.94.128.33]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5UMTnW2006469 for ; Wed, 30 Jun 2004 17:29:49 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mhub-c3.tc.umn.edu with ESMTP; Wed, 30 Jun 2004 17:34:56 -0500 (CDT) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO Message-ID: <40E34113.3090504)at(pobox.com> Date: Wed, 30 Jun 2004 17:39:15 -0500 From: Eric Bennett User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Michael CC: chemistry)at(ccl.net Subject: Re: CCL:software to convert XYZ format to PDB ? References: <003701c45ee8$ebad6710$b400a8c0@fedor> In-Reply-To: <003701c45ee8$ebad6710$b400a8c0@fedor> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Michael wrote: >Dear CCLers, > > > >I need to convert protein structure presented as XYZ (Cartesian coordinate >file) > >to the PDB file format. > >The problem is that many software packages can do the job but not >completely. > >In other words, when such software reads an XYZ file (see the fragment >below): > >... > >I would highly appreciate if somebody can point me to the reliable free >software for Windows. > > > I just wrote a perl script to do this a couple weeks ago... you can download a free perl interpreter for Windows from www.perl.com. http://www.perl.com/download.csp Here's the script, it's very short: http://abacavir.pharmacy.umn.edu/~bennette/software/text-to-pdb.txt -- Eric Bennett, Center for Drug Design, U of Minnesota The whole aim of practical politics is to keep the populace alarmed, and hence clamorous to be led to safety, by menacing it with an endless series of hobgoblins, all of them imaginary. -H.L. Mencken