[no subject]

[Mark Forster <forster%comp.nibsc.ac.uk |-at-| OHSTVMA.ACS.OHIO-STATE.EDU>]

 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 |-at-| uk.ac.nibsc.computing
 	rest of the world uses the reverse order system.
 		 forster |-at-| 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 |-at-| edu.ucsf.cgl
 Best Wishes
 Mark J. Forster
 p.s.	sending message to
 	chemistry%ccl.net |-at-| uk.ac.earn-relay