From owner-chemistry@ccl.net Sat May 14 08:14:01 2011 From: "Amrita Kumari amrita.g13,+,gmail.com" To: CCL Subject: CCL: TINKER software - cant you installed the binaries instead. Message-Id: <-44633-110514081250-8966-oMP3CNg20wGoQEXyXveq/Q^server.ccl.net> X-Original-From: Amrita Kumari Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 14 May 2011 17:42:40 +0530 MIME-Version: 1.0 Sent to CCL by: Amrita Kumari [amrita.g13,gmail.com] Dear Sir, Thankyou very much for your help. It has worked, I used .xyz input files from test directory and used the command given in .run file to test installation of TINKER and it has given the same result as whatsoever is there in .log file. Now one thing I am not getting that is how to visualize the output of Molecular Dynamics program. Like input .xyz file I am able to open in pymol but if I am using DYNAMICS program then how to visualize its output as a movie in pymol. what should be the format of output file and how to get it. I have read in TINKER manual that: Coordinate sets along the trajectory can be saved as sequentially numbered cycle files or directly to a TINKER archive .arc file. But I don't know how to get output as .arc file and how to visualize it as movie. Basically my aim is to use this software for some MD calculation and visualize the dynamics as movie. Thanks Amrita kumari Research Scholar IISER Mohali Chandigarh (INDIA). On Sat, May 14, 2011 at 5:58 AM, Arun Kumar Subramanian wrote: > hi > If you are a beginner to tinker and probably to computers, i would suggest > you to install the pre-compiled binaries. then all you need to do is just > define an environmental variable or just source the path every time you run > it. You can check the software by running a small minimization using the > minimize module of timer (it will be in the $tinkerhome/bin/minimize or > $tinkerhome/minimize path). But you need to create an xyz file with all > connectivities properly before you can use it. > > > i hope it helps you. > regards, > ArunKumar. S. > > > > On Fri, May 13, 2011 at 11:15 AM, Amrita Kumari amrita.g13#%#gmail.com > wrote: >> >> Sent to CCL by: "Amrita  Kumari" [amrita.g13[]gmail.com] >> Dear all, >> >> I am a new user of TINKER software. I have downloaded and installed it >> on my 32bit Linux system. But I don't know how to check whether it has >> been installed properly or not. I used command: ./compile.make, >> ./library.make and ./link.make for installation and it has produced >> the complete set of TINKER executables. But I don't know how to test >> this software means how to give input and get output. >> >> Thanks, >> Amrita Kumari >> Research Scholar >> IISER Mohali >> Chandigarh (INDIA).>>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>>      http://www.ccl.net/chemistry/sub_unsub.shtml>>      http://www.ccl.net/spammers.txt>> >> > >