From strasner@organik.uni-erlangen.de Fri Dec 18 04:12:58 1992 From: Thomas Strassner Message-Id: <9212180813.AA25518@derioc1.organik.uni-erlangen.de> Subject: MM2: atom type 50 To: CHEMISTRY@ccl.net Date: Fri, 18 Dec 92 9:13:47 MET Dear netters, I recently encountered a problem with MM2. In the last version of Prof. Allingers parameter set he uses parameter type 50 to represent benzene C. In former parameter sets benzene was represented by atom type 2. I'd be very interested in comments of anyone who has experience with those types. Where are the main differences between these types ? If you know any reference or paper dealing with these atom types, please tell me, cause I don't know when to use which type. Thanks in advance Thomas Strassner Institut of Organic Chemistry University Erlangen Germany e-mail: strasner@organik.uni-erlangen.de From fuhlerr@ze8.rz.uni-duesseldorf.de Fri Dec 18 10:13:04 1992 Message-Id: <199212181449.AA04185@oscsunb.ccl.net> Date: Fri, 18 Dec 92 15:36:31 CET From: Rainer Fuhler To: Subject: xray methylphosphonic acid Dear netters ! I'm desperately searching for the crystal structure of mathylphophonic acid. Help me please!!! Please send notes where to find it to kreidler@convex.rz.uni-duesseldorf.de. Thanx a lot Kay Kreidler Dept. of Inorganic Chemistry Heinrich-Heine-University Duesseldorf Germany From tudor@wucmd.wustl.edu Fri Dec 18 02:49:19 1992 Date: Fri, 18 Dec 92 08:49:19 -0600 From: tudor@wucmd.wustl.edu (Tudor Oprea) Message-Id: <9212181449.AA01233@wucmd> To: CHEMISTRY@ccl.net Subject: X-mas story The Nanokiller and the Molecular Policeman - a molecular modeller's story - 'Freeze your rotors and keep your torsions trans! You are uder arrest!' The molecular policman stood high mounting his processor, with a three-buttons mouse in his hand. 'I'm gonna add you to the database and keep you in there 'till you say the truth about the active conformation. I'm gonna find out who did it, when and where, and why. And you, dirty blocker, are going to tell me - if I have to minimize you 3000 iterations.' With a click on his mouse, the poor molecule was added to the database, while all its colors went pale hearing the menacing policeman. But he had to put in all suspects, because there were rumours that a nano-killer was at large. All the pharmaceutical industry was talking about it: the concurrents had a hired gun who was able to suicide all metallo-proteases at a nanomolar stroke. And the policeman was aware that unless he comes up with a description really quick, he might as well be out of job and loose his pension. So there he was, sitting in front of the CD-ROM, looking at Chemical Abstracts fingerprints (over 4 million suspects were listed) and expecting a miracle: the right structure in the right conformation. Hours before he looked at the Cambridge Crystallographic Prison, but unfortunately all metallo-compounds stored there were of no help: none of them was out of jail in the last 3 years, so no way they were involved. And now that all his hopes were vanishing, he was thinking of a way out. 'Oh, I wish I was a nuclear policemen! What a life that would have been - sitting in a megawatertank swimming all day long, waiting all my life for the protons to decay! Or a molecular artist - sitting all day long in front of an ESV terminal, painting molecules on the screen - looking all day long at those Hollywood beauties... All right, all right, I'm married, but THAT would have been my job, wouldn't it?' So there he was, feeling miserable, looking for the right angles and the right dipole, and the right configuration... When suddenly the screen flashed: RED ALERT. Suspect found in area P4' on the target. With a double click on his mouse and a few quick touches on the keyboard, entered the program, engaging his processors at full CPU power, and turning the prediction drive ON. If this was the correct structure, he wouldn't want to miss it for a million. He started PCA (Partial Circles Analysis) with a murderous look in his eyes: if this was the real suspect, he will get a heavy blow from the full force-field, and maybe they'll throw him in a dynamics run with 2500 water molecules - that will teach him a lesson! So he waited for all iterations to complete, and he fingered the keyboard for a few seconds - not to miss this structure in case another emergency would show up, and then he put the structure on screen. This molecule did not look very promising, except for that sulfur, which promised to mimick a transition state. Eversince heroin, all transition states were forbidden, except when induced by Yoga meditation, and all chemical transitions were carefully studied by law authorities and narcotic experts. He enlarged the image, and decided to quickly run an unrestricted Hartree-Fock calculation on that molecule, hoping to get the true coordination path. Otherwise, he would have to torture that molecule with a NMR study - think about all those proton impulses it would get - enough to tickle one to his death... So he launched a batch job, running in parallel on all available processors, glancing from time to time at the screen, as all those cycles went flashing by, and hoping that the output would give him the right geometry & answers. 'Oh, hi there, MP!' The green-eyed inspector was standing in the door, with an inquisitive look. 'What are you doing, following another lead on that nano- killer? Or just getting some partial charges for fun?' 'Well, sir, I'm looking at a transition state analog that seems to be involved in the metallo-protease inhibition. It certainly has no alibi, it has a bad record of competitive antagonism, and besides, it's not patented. I read him his rights, just in case, but until now he simulated no attempt to escape.' The molecular policeman was oiling his voice, hoping that this way he will get the inspector off his back before he would notice that Hartree-Fock was running in parallel processing. This, of course, was forbidden procedure, and it was condemned by the Geneva convention and the IUPAC manuals. But, hell, it was more faster and efficient than any single-CPU computation. So, just pretending he is busy, he turned off the screen just before a new cycle would show up and give the inspector a clue. 'Well, it's almost lunchtime, and we should be moving further with our research, MP, so I leave you to your duties, reminding you that we have a conference 2 weeks from now, and that the boss wants results before that, so that he can finish his grant proposal - otherwise you and I are both stuck, and remember...' 'Yeah, I know, we can loose our pension' mumbled the policeman as he carefully closed the door. He was on his way to the favorite time of the day: FOOD. This was the most rewarding fact of life, and as he stood in the row to take his plate, he watched the molecular inspector, who was having lunch in the canteen. He took his plate one floor up, where the 3D-QSAR people, (or the street-people - as they called themselves) were sitting near a bottle of Chianti Rosso, and singing old forgotten songs about long-forgotten heroes: Hansch, the hydrophobic man, Fujita, the man of QSAR, Cramer, the COMFA-gunner... And as he approached the eating room he realized that there was a party going on. It seemd like a red-cloaked wizard with a bag in his hand - and yes, it was Santa Claus. Of course, he realized, Christmas was due in 2 days, and the street people were celebrating together with their children. 'Well, maybe I shouldn't have come here with my plate, he thought, as no one was eating. So he stopped on the stairs, glancing at the crowd, and munching his bread and milk. He could not afford to stay while the killer was still at large. He strenghtened his will, took another quick bite, and went straight to his office. As he turned the screen on, he saw a flashing message - another email came while he was away. 'Damn those emails, all they do is keep you busy, and you can not ignore them, beacuse the computer will ask you to relpy asap!' So he took the keyboard and read the message - it was a question about molecular abortion, and wheather it should be allowed or not, so he just typed Y and sent it back - since he had no kids, he always thought abortion is the ultimate solution to stay out of trouble, and with that he turned back to his problem. And when he turned on the molecular viewer, the nano-killer stood there in all his splendor: its orbitals were of high energy, and the distribution was matching perfectly the coordination required by the enzyme. 'No wonder it works so well. I'd better run some check up first, but this time it seems that the molecular inspector will be pleased. There might be even a promotion on this!' So he faxed the robot-portrait and molecular fingerprints to all molecular policemen in the world - let the Interpol do the dirty work, it's Christmas anyway!' and with that he put the mouse back in its pad. It was high time for a cigar, and he fumbled his pockets for a light. 'Damn! I always forget that smoking is forbidden in this century'. So he went down to the canteen in search for a match. He knew it's not easy to find one, but with the help of a systematic search and a decent force field he would be able to. Merry Christmas, everybody! Tudor, 12/17/92. ** Copyright (c) Center for Molecular Design @ Washington University in St.Louis ** ** This work may not be reproduced in whole or in part for financial purposes ** ** without written consent of the author or the Center for Molecular Design ** ================================================================================ = Tudor Ionel OPREA = Tel. (1-314) 935 4672 = = Research Associate = Fax. (1-314) 935 4979 = = Washington University Center for Molecular Design = Email: = = Lopata Hall, Box 1099, One Brookings Drive = tudor@wucmd.wustl.edu = = St.Louis MO 63130 = = ================================================================================ From zottola@chemvax.chem.duke.edu Fri Dec 18 09:09:12 1992 Date: Fri, 18 Dec 1992 14:09:12 EST From: zottola@chemvax.chem.duke.edu To: CHEMISTRY@ccl.net Message-Id: <00965466.7471A280.31311@chemvax.chem.duke.edu> Subject: cartesian to pdb format I have a small problem and was wondering if anyone out here can help me. I have been examining a series of compounds with gaussian92. I thus have these compounds expressed as their cartesian coordinates. I would like to use Sybyl to visualize these structures. Does anyone know if a program exists to convert these cartesian coordinate files into Sybyl-readable pdb files? I was hoping to obtain this program through anonymous ftp rather than my research director's research grant. Thanks! -mark zottola zottola@chemvax.chem.duke.edu From shep@ss1.cray.com Fri Dec 18 08:45:17 1992 Date: Fri, 18 Dec 92 14:45:17 CST From: shep@ss1.cray.com (Shepard Smithline) Message-Id: <9212182045.AA00847@ss1.cray.com> To: chemistry@ccl.net Subject: free energy Dear Netters, Is there a handbook or other written source that lists solvation free energies of a variety of compounds? Please respond directly to me (shep@gravity.cray.com) as I do not wich to clutter the network. I will post a summary of the responses that I receive. Thanks, Shep Smithline