From chemistry-request@ccl.net Fri Aug 7 03:44:52 1992 From: Dan Severance Subject: Re: your mail To: rak@igor.caltech.edu (Robert A. Kumpf) Date: Thu, 6 Aug 92 20:38:01 EDT Organization: Laboratory for Computational Chemistry Status: R > > We have been trying to run a PMF calcuation for a system of two > solutes in a box of TIP3P water using BOSS version 2.7. The first > step of the simulation appears to work fine; however, all attempts > to continue the simulation using the option ISTART=3 have resulted > in values of 'Infinity' being written to the UP file. The ISTART=3 > option is the recommended choice for beginning the next step in a > free energy perturbation calculation. Has anyone encountered this > problem as well? Any suggestions for a fix would be greatly > appreciated. > Hi Bob, Try running the 311 simulation for 50,000 configs or so, and then instead of using 001 on the next step, use 011 to restart averaging (this will recreate the upfile). By that point the initial bad interactions which led to the infinities will have been resolved and furthur writes to the upfile will be fine. You can then do your normal 001 starts for the rest of the equilibration as usual... Dan Severance dan@omega.chem.yale.edu ! No big .sigs ! --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 04:23:31 1992 Date: 06 Aug 1992 22:50:46 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: new MacroModel mail exploder now available To: chemistry@ccl.net Status: R MMODINFO: THE MACROMODEL INFORMATION MAIL EXPLODER WITH ASSOCIATED ANONYMOUS FTP ARCHIVES. WHAT IS THE MMODINFO LIST? The MMODINFO LIST is an e-mail exploder which allows MacroModel users and computational chemistry researchers to exchange information and experience. The list and archives reside on a VAX 6420 running the VMS operating system at the University of Toledo. This list is not restricted and anyone is welcome to subscribe. It works on the principle, "WHAT ANYBODY POSTS, EVERYBODY GETS." All postings to this list are archived and available for downloading as described in the rules of the list which are automatically sent when you subscribe. HOW TO SUBSCRIBE. To subscribe to the MMODINFO List, send e-mail containing the message SUBSCRIBE MMODINFO to MMODINFO-REQUEST@UOFT02.UTOLEDO.EDU. ARCHIVES OF THE MMODINFO LIST. Currently, archives are accessible only via anonymous ftp at FTP.UTOLEDO.EDU (131.183.1.1) all mail sent to the list (in [.MMOD]). software and utility programs submitted by list subscribers (in [.CHEMISTRY.SOFTWARE]). positions offerred announcements (in [.CHEMISTRY.POSITIONS.OFFERRED]). positions wanted announcements (in [.CHEMISTRY.POSITIONS.WANTED]). DISCLAIMERS The list is organized as a service to MacroModel researchers. By posting to this list you agree that the content represents your personal opinion. In no event should the list administrator (Doug Smith), the University of Toledo, the authors of MacroModel (WCS et al.), its distributors (Distributed Chemical Graphics) or Columbia University be liable for the opinions or materials posted. The list administrator and others listed above are not reviewing the materials submitted to this list and cannot stop their distribution. LIST ADMINISTRATOR This list is operated by: Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 USA voice (419)537-2116 fax (419)537-4033 email dsmith@uoft02.utoledo.edu Additional support and problem solving by our VAX systems manager, Brian Nelson, and by: Peter S. Shenkin Department of Chemistry Barnard College New York, NY 10027 voice (212)854-1418 email shenkin@avogadro.barnard.columbia.edu or shenkin@cunixf.BITNET --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 09:33:06 1992 Date: 07 Aug 1992 07:17:08 -0400 (EDT) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: ACS Symposium on H-Bonding To: chemistry@ccl.net Status: R At the ACS National Meeting in Chicago, August 22-27, 1993 (a year from now) I will be chairing a symposium entitled "Modeling the Hydrogen Bond." We are now entering the planning stages for that symposium. If there is sufficient interest, I hope to have invited speakers, submitted oral papers, and a poster session. In order to assist in planning, I would ask that you, the readers of this mail exploder, help by letting me know if you are interested in speaking and/or presenting at this symposium. The more I know now, the more time and money I can ask for and the better the symposium will be. Please reply to me directly. I will summarize the invited speakers list at the appropriate time. Thank you. Doug Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 15:37:05 1992 Date: Fri, 7 Aug 92 11:40:39 -0400 From: kxb3@po.CWRU.Edu (Kenneth Butenhof) To: chemistry@ccl.net Subject: CHARMm .DCD distance extraction Status: RO Dear CHARMm user(s), I have a CHARMm MD data file (.DCD) from which I would like to extract a set of interatomic distances (for all frames). I have used the CORREL command for bond distance extractions, however this requires that the atoms be bonded (or at least have a atom types compatible for bonding). Of course, I could add new entries into the .PRM (.bin) file but this seems messy, and possibly dangerous. Is there a way to extract distances of unbonded sets of atoms, and generate statistics on the fluctuations? Unfortunately the CHARMm "package", on the CRAY at OSC, does not include the analysis modual - that would make it too easy. Yes, of course I should get Quanta -- but I don't have it now. -- any (other) suggestions would be greatly appreciated! -- Ken Butenhof Department of Pediatrics Case Western Reserve University Cleveland, Ohio 44106 --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 15:07:55 1992 Date: Fri, 07 Aug 1992 10:59:50 EDT From: breneman@XRAY.CHEM.RPI.EDU To: chemistry@ccl.net Subject: SYBYL User's Group BBS Invitation Status: RO From: MX%"" 7-AUG-1992 10:53:35.05 To: BRENEMAN CC: Subj: Return-Path: <@XRAY.CHEM.RPI.EDU:breneman@quant.chem.rpi.edu> From: Date: Fri, 7 Aug 92 10:54:47 EDT To: breneman@quant.chem.rpi.edu Date: Fri, 7 Aug 92 13:07:10 -0400 From: jle@world.std.com (Joe M Leonard) To: chemistry@ccl.net Subject: Wanted: Info on Sybyl atom type(s) Status: R For all you Sybyl guru's out there... What is the Sybyl atom type for the N in the nitro group? I can see N-pl3, since it's trigonal planar, or N-ar, which would be reasonable for nitrobenzene, or...? Looking at the published force field parameters seems to suggest that it really doesn't matter which I choose (even N-sp2 would work), but I'm interested in picking the type "correctly".. Thanks in advance, Joe jle@world.std.com --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 17:30:51 1992 Date: Fri, 7 Aug 92 14:06:55 EDT From: Weigang Huang To: CHEMISTRY@ccl.net Subject: help needed using gaussian 92: calculate istp freq. Status: R I am using gaussian 92 to calculate the vibrational frequency modes of boranes. I got the frequency modes of bh2sh , saved in a check point file. But I am having trouble using the 'ReadFc' and 'ReadIsotopes' options to get the frequency modes of different isotopomers of bh2sh. Since we don't have the manual for g92, my input file follows the manual of g90. Here are the input and part of the output: input: ------ $RunGauss %Chk=bh2sh.chk #freq=(ReadFc,ReadIsotopes) geom=checkpoint ChkBas bh2sh isotop#1 freq pvtz 0 1 no 11 32 1 1 2 ------ output: ------- ........ WANTED A FLOATING POINT NUMBER AS INPUT FOUND A STRING AS INPUT no ? Error termination in Lnk1e. ....... ------- Once I tried 'freq=ReadIsotopes' only, no error message about the input format but re-calculate frequecy from the scratch. Could somebody help me with this problem? BTW, does anybody know where can we get the manual of gaussian 92? Weigang Huang Chemistry department,the Ohio State University --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 18:23:50 1992 Date: Fri, 7 Aug 92 12:09:27 PDT From: d3f012@gator.pnl.gov Subject: Free Software To: CHEMISTRY@ccl.net Status: R 8/7/92 The semi-empirical electronic structure program Argus version 1.0 is now available by anonymous ftp on pnlg.pnl.gov When you get into the system you should go to the argus directory. The file is argus.tar I've included compiled executables for Sun4, SGI, IBM/6000, and Cray YMP. (Remember to use binary ftp) Additional notes: ---------------- I've disabled the geometry optimization in version 1.0. This code is being completely restructured to work better with the MD code (also not in version 1.0). I'd be happy to receive any constructive criticism on the program. I strongly encourage you to print the User Manual. Argus is free. However, it is Copyrighted and distributed under license. Make sure to read the CopyRight file and the License agreement included in the tar file. Enjoy. ---------------------------------------------------------------- Mark A. Thompson email: d3f012@pnlg.pnl.gov Sr. Research Scientist Molecular Science Research Center Pacific Northwest Laboratory PO Box 999, Mail Stop K1-90 Richland, WA. 99352 ---------------------------------------------------------------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 21:35:50 1992 Date: 7-AUG-1992 17:11:38.61 From: WSONNEN@EAGLE.WESLEYAN.EDU Subject: Re: CHARMm .DCD distance extraction To: chemistry@ccl.net Status: R One solution to extracting atomic distances from a CHARMm .DCD trajectory file is provided by the following: ------------------------ Note. The following example reads a .PSF file for your system and calculates the distances between atoms 1:6 and 530:542. This is a straight forward application of the DIST command (page 8 of Lecture #5, CHARMM COURSE by Bernie Brooks at the NIH---you'll have to contact him for your own copy of the notes [about 500 pages]. I'll fax you a copy of the relevant page if you need it). Good luck, Wayne Sonnen ------------------- * Script file produced by WAYNE * open write unit 7 Card name JUNK.LOG line outu 7 bomlev -2 bann OPEN READ UNIT 63 FILE NAME DNA_PSF.PSF READ PSF UNIT 63 OPEN READ UNIT 52 FILE NAME SI1_NO.DCD TRAJ IREAD 52 NREAD 1 EXPA NFILE 20 SET 1 1 LABEL L1 TRAJ READ COOR DIST CUT 11.0 SELE BYNUM 1:6 END SELE BYNUM 530:542 END INCR 1 BY 1 IF 1 LT 20.5 GOTO L1 STOP --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net --- From chemistry-request@ccl.net Fri Aug 7 22:54:33 1992 Date: Fri, 7 Aug 92 18:39:48 EDT From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: help needed using gaussian 92: calculate istp freq. To: chemistry@ccl.net Status: R Weigang Huang asked: I am using gaussian 92 to calculate the vibrational frequency modes of boranes. I got the frequency modes of bh2sh , saved in a check point file. But I am having trouble using the 'ReadFc' and 'ReadIsotopes' options to get the frequency modes of different isotopomers of bh2sh. Since we don't have the manual for g92, my input file follows the manual of g90. Here are the input and part of the output: input: ------ $RunGauss %Chk=bh2sh.chk #freq=(ReadFc,ReadIsotopes) geom=checkpoint ChkBas bh2sh isotop#1 freq pvtz 0 1 no 11 32 1 1 2 Once I tried 'freq=ReadIsotopes' only, no error message about the input format but re-calculate frequecy from the scratch. Could somebody help me with this problem? BTW, does anybody know where can we get the manual of gaussian 92? Weigang Huang Chemistry department,the Ohio State University This is an input incompatibility between Gaussian 90 and Gaussian 92, but we hope it is a change in the right direction. Instead of the silly line containing "no", for G92 you provide the temperature in kelvin and the pressure in atmospheres at which the thermochemical calculations are to be done. A value of zero for either quantity implies the default (standard temperature or pressure). Many G90 users requested the capability of reading in these values, hence the change. In hindsight, we should have continued to accept "no" as equivalent to 0.0,0.0 but we didn't think of that. You can order a manual from Gaussian, Inc. Call 412-621-2050. Questions about ordering Gaussian's products can be sent to info@gaussian.com. Questions about using the program and bug reports can be sent to help@gaussian.com Mike Frisch ------- --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everybody; CHEMISTRY-REQUEST@ccl.net --- coordinator only OSCPOST@ccl.net : send something from chemistry; FTP: www.ccl.net ---