From rvgloss@arcriba.edu.ar Sat Jul 16 18:53:54 1994 Received: from sic4.cnea.edu.ar for rvgloss@arcriba.edu.ar by www.ccl.net (8.6.9/930601.1506) id SAA02832; Sat, 16 Jul 1994 18:37:07 -0400 Received: by sic4.cnea.edu.ar (/\==/\ Smail3.1.25.1 #25.4) id ; Sat, 16 Jul 94 19:38 GMT-3:00 Received: by arcriba.edu.ar (5.59/25-eef) id AA03942; Sat, 16 Jul 94 19:34:37 ARG Received: by arcriba.edu.ar (5.59/25-eef) id AA03932; Sat, 16 Jul 94 19:34:35 ARG Message-Id: <9407162334.AA03932@arcriba.edu.ar> From: rvgloss@arcriba.edu.ar (Daniel Glossman) X-Mailer: SCO System V Mail (version 3.2) To: chemistry@ccl.net Subject: MOPAC latex manual Date: Sat, 16 Jul 94 19:34:33 ARG Dear netters: Is there any available latex version of the MOPAC manual? If so, how to get it? Please answer directly to me : rvgloss@arcriba.edu.ar Thanks in advance Daniel Glossman From heather@ramana.chem.yale.edu Sat Jul 16 19:17:03 1994 Received: from ramana.chem.yale.edu for heather@ramana.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id SAA02844; Sat, 16 Jul 1994 18:42:39 -0400 Received: by ramana.chem.yale.edu; Sat, 16 Jul 94 18:42:38 -0400 Date: Sat, 16 Jul 94 18:42:38 -0400 From: Heather Carlson Message-Id: <9407162242.AA26315@ramana.chem.yale.edu> To: chemistry@ccl.net Subject: summary of surface area&volume I was asked to post a summary of the responses I received about finding molecular surface areas and volumes. I would like to thank everyone who responded, especially those who offered copies of their own programs! We've decided to use Fred Richards programs (thanks C. S. Raman) since they're a standard & he's across the science courtyard!! Heather Carlson heather@ramana.chem.yale.edu SUMMARY: ------------------------------------------------------------------------- From: jle@world.std.com (Joe M Leonard) I'm not sure whether Yale ever got Spartan, but if it has, we calculate the area and volume using the same radii. There are other codes floating about in the PD or at QCPE, which you can probably recompile with changed radii... Joe Leonard jle@world.std.com ------------------------------------------------------------------------- From: RAVANTTI@msvax.mssm.edu The program GRASP from Anthony Nicholls, nicholls@cuhhca.hhmi.columbia.edu should have an answer to your problem. Liisa Laakkonen ------------------------------------------------------------------------- From: maxv@iserver.pdl.com (Max Vasquez) Take a look at a program by Frank Eisenhaber; information below. Good luck. Thank you very much for your interest in the paper "Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency" published in Journal of Computational Chemistry, v. 14, N11, (1993), pp.1272-1280 by Frank Eisenhaber and Patrick Argos and the associated program ASC. The program text in standard C for UNIX systems can be obtained from the author in the following way (for academic use): (1) ftp 192.54.41.168, the ftp-server is falcon.EMBL-Heidelberg.DE; (2) login: ftp, during login give your E-mail address as password; (3) change to the directory /pub/asc; (4) move all files of this directory to your site, do not name your local directory asc (better ASC or something else to avoid interference with the executable asc !!); (5) execute asc.call (calls make to make executable "asc") and (6) use manual.int as introduction and manual.lib as command reference; Since the time of the publication, a few improvements have been introduced. As a result, the CPU-consumption was further reduced. The three time thresholds for the analytical surface calculation in Tables I and II can be corrected to the following values: (1) 1PPT: 0.24, 1.74, 1.97 (2) 4PTI: 0.71, 3.66, 4.02 (3) 2PCY: 1.97, 7.38, 8.14 (4) 2RHE: 2.00, 7.72, 8.80 (5) 3FXN: 3.54, 11.43, 13.13 (6) 2UTG: 3.44, 11.29, 12.86 and (7) 1CRN: 0.39, 2.46, 2.71. The time consumption had been measured for an R3000 processor in a SGI-workstation. The overall time dropped by about 40\% compared with the data in the article, e.g. the cpu-time for 1CRN decreased from 4.27 seconds to 2.71 seconds.a >From time to time I may change a few files at the ftp site because some of the users or I myself find some strange behaviour. As long as the changes are minor and, especially, do not touch the surface calculation section, the version number will not be changed. It might be useful to update your local version from time to time. The program had been tested for ULTRIX on DEC-stations and for IRIX on SGI-computers. It runs also under SunOS 4.1.3 if compiled with gcc ! Please, contact me by E-mail, if you have suggestions, problems or questions. Sincerely, Frank Eisenhaber E-mail : IN%"EISENHABER@EMBL-Heidelberg.DE" ------------------------------------------------------------------------- From: dirk@rulglj.LeidenUniv.nl (Dirk Huckriede) I posted a similar request like yours say half a year ago and got quite a number of responses. One of the (Fortran) programs I obtained is able to calculate surfaces and volumes in one run without altering the input etc. I think it is best suited for your purposes. I left it at our anonymous ftp server for you to collect: ftp rulglj.leidenuniv.nl anonymous your mail-adres cd pub/heather binary get volume1.tar If you are not able to use ftp, please mail be, I can send you the file uuencoded (the system manager won't like it though). Bye ! ------------------------------------------------------------------------- From: schaefer@tammy.harvard.edu (Michael Schaefer) I can't give you advice how to use Sybyl for your task, but I have a program that calculates the solvent inaccessible volume of a molecule AND the solvent accessible surface. Volume and surface are calculated for each atom (output format: pdb, volume and surface in the 4th and 5th data column). If you are interested, let me know. Michael Schaefer ------------------------------------------------------------------------- From: David White I am interested in getting into the derivation and coding of analytical algorithms to calculate molecular surface areas and volumes. The data you ask for could be vital in my determining the effecacy of such an algorithm. Please summarize the repsonses! Thanks Dave ------------------------------------------------------------------------- From: raman@bioc01.uthscsa.edu (C.S.RAMAN) What you need are the programs ACCESS (for calculating solvent accessible surface areas) and VOLUME from Fred Richards at Yale. I suggest that you contact Art Perlo (perlo@hhvms8.csb.yale.edu) to obtain an academic license (free for academia!). Since you are in New Haven there should be no problem. ACCESS will let you define any probe radius and is pretty straight-forward to use. Yet another package called MSP (Molecular Surface Package) is available from Mike Connolly (Connolly@netcom.com) for detailed dissection of surfaces. Finally, GRASP (from Tony Nichols, Columbia U.) also has various features to manipulate surfaces. Hope this helps Cheers -raman ------------------------------------------------------------------------- From: Volkhard Helms I have used the program GRASP of Anthony Nicholls from Barry Honig's group a few times (I'm no expert with it though) and it is very easy to calculate both molecular surfaces and volumes with it and also to display them. It uses a certain set of vdW parameters for both cases, and one can also modify this set. Hope this helps. Volkhard Helms ------------------------------------------------------------------------- From: hurst@hyper.hyper.com (Graham Hurst) The ChemPlus set of extensions to HyperChem includes a QSAR Properties module that can calculate surface area and volume using the same radii. The radii are kept in a text file that you can edit if you want to use different values. You can also drive the calculation from a Windows spreadsheet program (such as Excel) to collect volumes and surface areas for a set of molecules into a spreadsheet. It can also calculate hydration energy, Log P, refractivity, polarizability, mass and partial atomic charges using published empirical methods. For more information send email to info@hyper.com. Cheers, Graham ------------------------------------------------------------------------- From: chen@agouron.com (Chris Chen) Hi, You may like to try QUANTA from MSI and VOID from QCPE for your calculation. Chris chen@agouron.com ------------------------------------------------------------------------- From: HUTCHINS%CMDA Another program to try is SAVOL by Robert Perlman at the University of Texas at Austin. I believe this is readily available from him. Charles Hutchins Abbott Laboratories ------------------------------------------------------------------------- From: "J. Eric Slone" Please take a look at a product which I market, a demo of which is in ccl.net, /pub/chemistry/software/MS-DOS/MOLGEN-demo. It can handle what you are looking for, plus a lot more. And it will read your Sybyl files! Let me know if you are interested (academic pricing is $290). Eric *************************END OF SUMMARY**********************************