Subject: amber4.1

From: <[email-masked]>
Date: Wed, 22 Mar 1995 17:35:04 -0800

It gives us great pleasure to announce the release of  AMBER  4.1.
    This code is a joint effort of the Kollman group at UCSF, the Case
    group at The Scripps Research Institute, David Pearlman of  Vertex
    Pharmaceuticals and David Ferguson of the University of Minnesota.
    
    We are very excited about the fact that this version of AMBER will
    be  jointly supported by the company Oxford Molecular (OM) as well
    as  by  the  various  authors.   Oxford   Molecular   will   offer
    commercial-level  support  and  update  services and the option of
    bundling AMBER with their other complementary software.
    
    We expect that this partnership will combine the best  of  univer-
    sity science with the benefits of commercial ease of use.  We  are
    very pleased with this arrangement  because:  (1)  commercial  and
    noncommercial users can receive standalone AMBER exactly as before
    or get it from OM (the price for standalone remains unchanged from
    4.0); (2) source code will be distributed from both places, as has
    always been the case; (3) Oxford Molecular can  also  include  the
    programs  compiled  and  ready  to  run;  and  (4) OM will help us
    develop the graphical interface program LEAP to their  "Gold  Pro-
    duct" level. Contact information for OM is given below.
    
    AMBER 4.1 has a number of exciting new features:
    
     (1)   The free energy module, GIBBS, has the capability of calcu-
           lating  free  energy derivatives, free energy components by
           residue and  free  energies  involving  non-additive  force
           fields.  It also supports free energy perturbation, thermo-
           dynamic integration and slow growth within  both  dual  and
           single topologies. PMF and constraint contributions are now
           fully   implemented   within   thermodynamic   integration.
           Optional dual cutoff and alternate cutoff for the perturbed
           group have been implemented.
    
     (2)   TIP3P water systems in both GIBBS and the molecular  dynam-
           ics  /  NMR  fitting program SANDER have been speeded up by
           the incorporation of Shuichi  Miyamoto's  analytical  shake
           for  three-point water, and the water-water non-bonded code
           has been made more efficient.  This speedup can be as large
           as  30%.  Both programs have been parallelized under a gen-
           eralized  MPI  (Message   Passing   Interface)   for   MIMD
           architectures with the contributions of Jim Vincent and Ken
           Merz of Penn State, and also  for  shared  memory  parallel
           machines with the help of Silicon Graphics Incorporated.
    
     (3)   A fast, "particle mesh" implementation  of  the  Ewald  sum
           method  for simulating an infinite lattice has been contri-
           buted by Tom Darden of the National Institute  of  Environ-
           mental  and  Health  Science and installed in SANDER by Tom
           Cheatham (UCSF) and Darden.
    
     (4)   SPASMS, an MD and perturbation program originally developed
           by  David  Spellmeyer  of  UCSF (now at Chiron), Bill Swope
           (IBM) and Erik Evensen (now at Harvard), is  being  further
           developed  mainly  by  David  Ferguson of the University of
           Minnesota.  It incorporates a number of new approaches  not
           available in SANDER and GIBBS.
    
     (5)   INTERFACE, a  program  written  by  David  Pearlman,  which
           allows an efficient way to set up multiple and complex runs
           involving the computationally intensive parts of AMBER 4.1,
           is  being  distributed  with  the rest of the code. It is a
           general program that allows front ends to be generated  for
           other programs as well.
    
     (6)   LEAP, the graphical user  interface  written  by  Christian
           Schafmeister  (UCSF),  has  been  significantly improved by
           Bill Ross and Vladimir Romanovski, and is included in AMBER
           4.1.   It  has had a long, ongoing debugging process but we
           feel it is now sufficiently robust for general use.
    
     (7)   The new additive force field,  developed  mainly  by  Wendy
           Cornell  and  Piotr  Cieplak (manuscript in press in JACS),
           will be available with the code.  The /dat  directory  will
           also support the force fields of Weiner et al. (1984-United
           atom; 1986-All atom) and OPLS/AMBER  by  William  Jorgensen
           and  co-workers.  We hope to make other force fields avail-
           able as well (e.g. the Merz group  and  Rob  Woods  of  the
           University of Georgia have carbohydrate ones).  The Cornell
           et al. force field will  be  publically  available  through
           anonymous ftp, but AMBER 4.1 users will have it in advance.
    
     (8)   The code to calculate RESP charges (Bayly et al. JPC,  1993
           and  Cornell  et al.,  JACS, 1993) will be distributed with
           AMBER 4.1
    
     (9)   A number of new features related to  structural  refinement
           using  NMR  data  have  been  added to the SANDER and NMODE
           modules, including order parameter analysis, spectral simu-
           lation,  quasiharmonic  refinement  and  improved simulated
           annealing facilities.
    
    If you are interested in obtaining a copy  of  AMBER  4.1,  please
    contact  Willa  Crowell  of  UCSF  ([email-masked])  or Oxford
    Molecular at one of the following sites:
    
         USA:
              California:  toll free  1-800-876-9994
                   phone (415) 962 7300   fax (415) 962 7302
                   email [email-masked]
              Oregon:      toll free  1-800-544-6634
                   phone (503) 526 5000   fax (503) 526 5099
                   email [email-masked]
    
         UK:       phone  +44 1865 784600        fax +44 1865 784601
                   email  [email-masked]
    
         France:        phone  +33 1 69 33 35 90      fax +33 1 69 30 41
                   email  [email-masked]
    
         Germany:  phone  +49 9131 8796 0        fax +49 9131 8796 11
                   email  [email-masked]
    
    Thank you for your interest and continued support.

                          Sincerely yours,

                           Peter Kollman
                             Bill Ross
                           Jim Caldwell
                            Tom Cheatham
                           David Pearlman
                           David Ferguson
                             David Case