From chemistry-request@ccl.net Thu Feb 6 04:59:32 1992 From: Mark Forster Date: Thu, 6 Feb 92 09:30:24 GMT To: chemistry@ccl.net Status: R Subject: request for AMBER information MAIL FROM Mark .J. Forster, Informatics Laboratory, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK. Tel (0707) 54753 Fax (0707) 46730 e-mail from within the u.k. use forster@uk.ac.nibsc.computing rest of the world uses the reverse order system. forster@computing.nibsc.ac.uk Dear Carlos, I dont have any information of MOLTECH but have been using AMBER for about 2 years. AMBER (assisted model building with energy refinement) is a program for molecular mechanics and dynamics. The program deals largely with proteins and nucleic acids because existing parameters and residue types for these are well established. We have been using the program to model carbohydrates using parameters recently published by Steve Homans at the University of Dundee. AMBER currently stands at version 4 and offers the following capabilities. 1. Build molecule, solvate check params etc. Modules PREP/LINK/EDIT/PARM 2. Static energy analysis - ANAL MODULE 3. Energy minimisation and Molecular dynamics - MINMD MODULE 4. Normal mode analysis - NMODE module 5. Generate nucleic acid coordinates - NUCGEN module 6. Minimisation, MD and NMR based structure refinement- SANDER module. 7. Free energy perturbation calc. - GIBBS module. Given the Hardware that you mention I think it would run without any problems on a SparcStation. AMBER has good and bad points that you must consider. GOOD: 1. Respected, High quality force field that covers (now) proteins, DNA/RNA, carbohydrates not many packages can model a glycoprotein for example. 2. Low cost - only $200 to academic users. If you change your computing hardware you can transfer the license ageement (so I understand) but at $200 it is cheap enough to get a new and updated copy. 3. Well supported - bugfixes available by e-mail to those who subscribe to the AMBER mail reflector. 4. Under constant development - witness the new features in AMBER 4 and pointers to future developments such as atom polarization effects. BAD: 1. Non graphical and not very easy to use. The fact that it is non graphical aids portability and is not much of a loss. The most painful features of using AMBER are (a) use of formatted FORTRAN input - meaning the numbers in the control files make little sense without the manual open at the right page, (b) the extreme pain of generating the tree structure required for the AMBER module PREP that generates a new residue type. LINK/EDIT/PARM are bad enough but PREP is the bottleneck to my mind. Version 4 removes the need for formatted input for some modules. We have been developing a X11/XLIB based graphical interface that allows a PDB file to be loaded and semi-automatically generates enough information to write an input file for PREP. An e-mail contact name for further AMBER information is BILL ROSS ross@edu.ucsf.cgl Best Wishes Mark J. Forster p.s. sending message to chemistry%ccl.net@uk.ac.earn-relay From chemistry-request@ccl.net Thu Feb 6 15:38:34 1992 Date: Thu, 6 Feb 92 21:13:48 +0100 From: bayard@chitheo1.univ-lyon1.fr (BAYARD Francois URA805 LYON 72 44 82 79) Subject: old to fortran 77 To: chemistry@ccl.net Status: R I 'd like to suppress many goto which are in an old fortran source by if ... then ... else Is there a ftp server or somebody having this product ? I'll prefer the automatic way to avoid mistakes ------ Francois BAYARD | e-mail bayard@chitheo1.univ-lyon1.fr UNIVERSITE CLAUDE BERNARD LYON 1 | tel (+33) 72 44 82 79 43 Bd du 11 Novembre 1918 | fax (+33) 72 44 08 03 F-69622 VILLEURBANNE - FRANCE | -------------------------------------------------------------------------- From chemistry-request@ccl.net Thu Feb 6 19:13:24 1992 Date: Fri, 7 Feb 1992 9:44:17 +1100 (EST) From: SATYAM_P@SUMMER.CHEM.SU.OZ.AU Subject: Enquiry -Theory of NMR Parameters (Programs/Authors) To: chemistry@ccl.net Status: R Dear Fellow Netters, Does anybody know of Latest email/contact address of I.Ando or G.A.Webb (Author of Book: Theory of NMR Parameters) ? OR Does anyone of you have the programs given at the end of the above mentioned book ? Is it possible to ftp these programs ? Thanks in advance Satyam ----------------------------------------------------------------- Dr. Satyam Priyadarshy Department of Theoretical Chemistry University of Sydney, Sydney NSW 2006, Australia Phone : 61-2-692 4785 (w) 61-2-550 5868 (h) Fax 61-2-692 3329 email : satyam_p@summer.chem.su.oz.au ------------------------------------------------------------------