From UDIM018@FRORS31.bitnet Mon Apr 8 11:07:07 1993 Message-Id: <199304081310.AA21833@oscsunb.ccl.net> Date: 08 Apr 93 15:07:07 EDT From: Subject: RS/6000 window version of Xmol To: chemistry@ccl.net E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-44-27-41-17 (lab);44-27-38-66(University) e-mail UDIM018 at FRORS31.BITNET I am looking for an RS/6000 windows version of Xmol. Could the distributer of the program send me a message of you location. Evleth From mlorenz@ecn.purdue.edu Thu Apr 8 07:34:55 1993 Date: Thu, 8 Apr 93 12:34:55 -0500 From: mlorenz@ecn.purdue.edu (Michael Lorenz) Message-Id: <9304081734.AA04079@cn.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: MOPAC-IRC calculation Dear Netters, I am using an older version of MOPAC (4.0) and I am attempting to do an IRC calculation using the restart file from a force calculation. However, an end-of-record is being encountered by subroutine DFPSAV when it attempts to read the restart file. Has anyone ever encountered this problem? If so, how would you recommend to correct this. Thanks in advance, Mike Lorenz Graduate Student Purdue University p.s. The administration is currently looking into obtaining a current version of MOPAC (6.0 or 7.0) From jk@iris68.biosym.com Thu Apr 8 04:50:14 1993 Date: Thu, 8 Apr 93 11:50:14 -0700 From: jk@biosym.com (Kottalam) Message-Id: <9304081850.AA15923@iris68.biosym.com> To: chemistry@ccl.net Subject: simulated annealing I did not respond to the original request, since it seemed specific to CHARMM. But now the discussion has gotten more general. For small molecules, one can hope to explore a significant number of local minima with simulated annealing. However, for macromolecules such as proteins, additional information is needed to supplement the molecular topology information. One source of the additional info. is from NOE experiments. 1) One way to perform SA is by heating and cooling. This is more appropriately called a "Boltzman jump" because the kinetic energy helps the molecule jump over energy barriers to explore neighboring local minima. Only a small region in the vicinity of the starting structure can be explored this way. 2) Clore, Nigles and Gronenborn used another equivalent method. They scaled down all the forcefield parameters (force constants) to make the atoms of the molecules more fluid. Then they brought the parameters back to the proper values in presence of NOE constraints. This method is provided with Biosym's NRMchitect. The first method is useful for exploring almost all conformational space of a small molecule. It is also useful in a macromolecular context if one wishes to remain close to the starting conformation. This situation arises when the starting structure was obtained from distance geometry calculations or from homology modeling. The second method takes apart the atoms of a molecule and puts them back together. The long range NOE restraints are activated first. The protein folds rapidly due to the NOE restraints. Finally, the bond lengths and angles are adjusted to their correct values after the secondary structure has formed. Kottalam jk@biosym.com (619) 546 5366