From: "Graham Wills-Johnson" Organization: RMIT Applied Physics To: hein@chemie.uni-konstanz.de CC: hyperchem@hyper.com Subject: Re: Torsion Angles Date: Fri, 19 Mar 1999 10:00:34 EST-10ESUT > From: Frank Schaper > To: hyperchem@hyper.com > Subject: Torsion Angles > Date: Thu, 18 Mar 1999 12:26:33 +0100 > Reply-to: Frank Schaper > Dear Hyperchem-Users, > is there a script command, which is able to write the value of an > selected bond-torsion into a Hyperchem-Logfile. I have checked the > handbook and the online-help, but have not found anything. If you have your output messages routed to .log then following the select command which selects the 4 atoms forming the dihedral bond angle, followed immediately by query-value status-message does the trick. I posted a complete script in answer to the question about setting angles remotely across a substituted acetylene, in which this is done twice, several weeks ago - it should still be available on the user group somewhere. Graham Wills-Johnson Dept Applied Chemistry RMIT Melbourne, Australia. rcmwj@bunyip.ph.rmit.edu.au > Yours, > > Hein > > Frank H. Schaper - AG Brintzinger - Universitaet Konstanz > email : Frank.Schaper@uni-konstanz.de > Frank@Schaper.com > s-mail : Frank Schaper - AG Brintzinger - Universitaetsstr. 10 > 78434 Konstanz > From: =?iso-8859-1?Q?Márcio?= Cyrillo To: Frank Schaper CC: hyperchem@hyper.com Subject: Re: Torsion Angles Date: Thu, 18 Mar 1999 18:14:23 -0300 Dear Frank, There is no such script command, though you can write the selection-value script variable to any file you want, that is, you can simulate the command you wanted quite readly: The script that will work, I guess, is: select-none selection-target atoms multiple-selections YES select atom a1 m1 select atom a2 m1 select atom a3 m1 select atom a4 m1 # so, we have four selected atoms, thus a dihedral # now what interests append-omsgs-to-file C:\mydir\myfile.log query-value selection-value omsgs-not-to-file I hope this helps, any further questions, be my guest, regards, Marcio. Frank Schaper wrote: > Dear Hyperchem-Users, > is there a script command, which is able to write the value of an > selected bond-torsion into a Hyperchem-Logfile. I have checked the > handbook and the online-help, but have not found anything. > Yours, > > Hein > > Frank H. Schaper - AG Brintzinger - Universitaet Konstanz > email : Frank.Schaper@uni-konstanz.de > Frank@Schaper.com > s-mail : Frank Schaper - AG Brintzinger - Universitaetsstr. 10 > 78434 Konstanz --------------C3B96387A372E24A315C7A6B Content-Type: text/x-vcard; charset=us-ascii; name="cyrillo.vcf" Content-Description: Card for Márcio Cyrillo Content-Disposition: attachment; filename="cyrillo.vcf" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by ifi.unicamp.br id SAA29637 begin:vcard=20 n:Cyrillo;M=E1rcio tel;work:Universidade Estadual de Campinas x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:cyrillo@ifi.unicamp.br fn:M=E1rcio Cyrillo end:vcard --------------C3B96387A372E24A315C7A6B-- From: Frank Schaper Reply-To: Frank.Schaper@uni-konstanz.de To: hyperchem@hyper.com Subject: Torsion Angles Date: Thu, 18 Mar 1999 12:26:33 +0100 Dear Hyperchem-Users, is there a script command, which is able to write the value of an selected bond-torsion into a Hyperchem-Logfile. I have checked the handbook and the online-help, but have not found anything. Yours, Hein Frank H. Schaper - AG Brintzinger - Universitaet Konstanz email : Frank.Schaper@uni-konstanz.de Frank@Schaper.com s-mail : Frank Schaper - AG Brintzinger - Universitaetsstr. 10 78434 Konstanz From: Todd Richmond To: hyperchem@hyper.com Subject: dynamics snapshots Date: Mon, 1 Mar 1999 16:02:53 -0800 Greetings, We are doing some dynamics calculations on a protein, and would like to get the lowest energy structure to measure some distances. We get the simulation to run OK, and can get a .csv file with the energies (that's how we are identifying the lowest). The problem is we cant figure out how to get at that time point's coordinates. We can playback the simulation, and if we could just stop at the desired time point, we would use that set of coordinates. I've tried to look at the .snp file, but it doesn't appear easy to parse. So...is there a way to either parse the .snp file (we'd love to be able to get interatomic distances out directly for the selected atoms), or have the simulation save just the lowest energy conformations? Or is there a better way to do this whole thing? ANy ideas appreciated. Thanks, Todd Todd A. Richmond, Ph.D. Assistant Professor of Chemistry The Claremont Colleges http://enzyme.claremont.edu