From owner-chemistry@ccl.net Fri Aug 5 06:14:37 2005 From: "CCL" To: CCL Subject: CCL: Using TINKER with AMBER99 force field ! Message-Id: <-28949-050805060601-24303-UGblJhHCRhLlm/aY0tUb9g^_^server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" Hello, I noticed that amber99.prm in TINKER doesn't have parameters for protonated Aspartic acid though these are present in amber99. It seems these can be added to the amber99.prm - I tried but tinker can't read those new parameters. Has anybody done something like this (adding new parameters to .prm files in TINKER)? I would appreciate any response. If necessary I can show the changed amber99.prm file. thanks, Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati Phone: 91-361-258-2213 (office) e-mail: pradipta^_^iitg.ernet.in web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Fri Aug 5 14:34:03 2005 From: "CCL" To: CCL Subject: CCL: Test of Intel Fortran 9.0 Message-Id: <-28950-050805115540-23308-UGblJhHCRhLlm/aY0tUb9g=-=server.ccl.net> X-Original-From: Christoph van =?iso-8859-1?Q?W=FCllen?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Mime-Version: 1.0 Sent to CCL by: Christoph van =?iso-8859-1?Q?W=FCllen?= I had to look for a new Fortran compiler for an opteron box with large memory, so I tried the Intel Fortran compiler 9.0 as it can produce 64-bit code. I would like to share my experience: As to the performance, nothing special (similar to earlier versions according to my few and lousy measurments). I could compile MOLPRO (64-bit, with 64-bit integers) and pass the test suite (this was where I needed the compiler for, so I am happy). For a recent version of TURBOMOLE, the test suite is not passed (program ricc2 chokes on each test), both if compiled for 32-bit and 64-bit address space (compilation without any optimization does not improve it). Compared to Intel Fortran 8.x, this looks not too bad, but for 32-bit applications, my favourite compiler remains Intel 7.1. However, there is some hope that 9.x for some x>0 may pass my Q.C. Yours, +---------------------------------+----------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | | | D-10623 Berlin, Germany | Christoph.vanWullen=-=TU-Berlin.De | | http://www.chemie.tu-berlin.de/vanwullen | +---------------------------------+----------------------------------+ --