From CTARG@Levels.UniSA.Edu.Au Tue Jul 20 22:28:08 1993 Date: Tue, 20 Jul 1993 12:58:08 +0930 From: CTARG@Levels.UniSA.Edu.Au Subject: Zr(SiO4) and Al(OH)3 molecular modelling To: chemistry@ccl.net Message-Id: <01H0RLGCZLO28WW8JI@Levels.UniSA.Edu.Au> I'm just starting to try and model some Zr(SiO4) and Al(OH)3 systems and need some mollecular mechanics parameters for Zr and Al for these or related systems. Does anybody know of any references or groups working in this area? Thanks, Andrea. From watson@Kodak.COM Tue Jul 20 03:58:16 1993 From: watson@Kodak.COM (Ian Watson) Message-Id: <9307201158.AA05501@icts01.Kodak.COM> Subject: Virtual Memory To: chemistry@ccl.net Date: Tue, 20 Jul 1993 07:58:16 -0400 (EDT) As a follow on the discussion on virtual memory, I am reminded of a little experiment we did some time ago. A Fortran programme declared an array of 40 million double precision variables (over 320MB of data). From memory, by accessing only every 5000'th element, do 100 i = 1, 40000000, 5000 x(i) = .... the programme ran successfully to completion on my Indigo, with only 48MB of RAM and a 40MB swap space. How is this possible? Well, as others have pointed out, the resource is allocated as it is accessed, and by fortuitous coincidence with the page size of the operating system, the programme ran to completion. Reducing the stride to 2000 caused the programme to be killed as this required the allocation of more pages than could be physically stored. Ian Watson (716) 722 1165 (voice) Eastman Kodak R&D (716) 477 5879 (fax) 5th Floor Bldg 83 watson@kodak.com Rochester NY 14650-2221 USA Usual disclaimers.... From george@archimedes.cray.com Tue Jul 20 03:54:35 1993 Date: Tue, 20 Jul 93 08:54:35 CDT From: george@archimedes.cray.com (George Fitzgerald) Message-Id: <9307201354.AA07629@archimedes.cray.com> To: chemistry@ccl.net, dave@carbon.chem.csiro.au Subject: DFT/ab initio calcs on tungsten Dear Netters, In response to inquiries about DFT computations on heavy elements, I would like to add a few points about DGauss. DGauss now incorporates relativistic pseudopotentials, as described in J Chem Phys 98, 8710 (1993). This extends DGauss functionality to all atoms excpet the La and Ac series. However, this project was funded by our UniChem consortium, and so the code will not be available to non-constrium members until the next release in 4Q 93. Interested persons can contact me for additional information. George Fitzgerald Cray Research, Inc. george@gravity.cray.com From d3f012@pellucidar.pnl.gov Tue Jul 20 00:01:20 1993 Date: Tue, 20 Jul 93 07:01:20 -0700 From: d3f012@pellucidar.pnl.gov Subject: Tungsten, Xenon, etc. To: chemistry@ccl.net Message-Id: <9307201401.AA05781@pellucidar.pnl.gov> David Wrinkler wrote: >I have some inorganic compounds which contain tungsten and cobalt. I note >that >all of the codes in Unichem, including Dgauss, will only handle elements up to >Xe. Do any semiempirical or ab-initio (especially DFT) codes handle tunsgten? The program ZINDO, from Mike Zerner's group at the University of Florida, can treat elements through the lanthanides and actinides. Presumably, they may have a set of INDO1 parameters for the tungsten and xenon... While INDO1 is not the best Hamiltonian for geometries, properties, etc. it is probably the only semiempirical Hartree-Fock based method that could treat elements further down the periodic table. I believe ZINDO has now gone commercial. You can find out by sending email to Rajiv Bendale (bendale@qtp.ufl.edu). Mark ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From J_BROWN@uvmvax.uvm.edu Tue Jul 20 05:57:00 1993 Date: Tue, 20 Jul 1993 10:57 EST From: J_BROWN@uvmvax.uvm.edu Subject: fortran "magic" and memory allocation ? To: chemistry@ccl.net Message-Id: <01H0RHA2GZBK001ULN@uvmvax.uvm.edu> Ian Watson writes: > As a follow on the discussion on virtual memory, I am reminded > of a little experiment we did some time ago. > > A Fortran programme declared an array of 40 million double > precision variables (over 320MB of data). From memory, by > accessing only every 5000'th element, > do 100 i = 1, 40000000, 5000 > x(i) = .... > the programme ran successfully to completion on my Indigo, with only > 48MB of RAM and a 40MB swap space. > How is this possible? Well, as others have pointed out, the resource is > allocated as it is accessed, and by fortuitous coincidence with the > page size of the operating system, the programme ran to completion. > Reducing the stride to 2000 caused the programme to be killed as this > required the allocation of more pages than could be physically stored. My question is what happens when you try to dimention the FORTRAN array, does the statement: DIMENTION X(40000000) actually compile without an "out of memory" error ? Also, did you check the array elements ? For example, does the statement: WRITE(*,*) X(40000000) print the correct stored value at this array element, or do you get "trash" back. Signed, "Doubting Thomas" aka. Jay Brown From kryan@paulaner.cray.com Tue Jul 20 09:06:13 1993 Date: Tue, 20 Jul 93 14:06:13 CDT From: kryan@paulaner.cray.com (Karen L. Ryan) Message-Id: <9307201906.AA19569@paulaner.cray.com> To: george@archimedes.cray.com Subject: DFT/ab initio calcs on tungsten > However, this project was funded by our UniChem consortium, and so > the code will not be available to non-constrium members until the > next release in 4Q 93. In the future you should be more careful about the date of the next UniChem product release. We may not release anything until 1Q94. -kr From srheller@asrr.arsusda.gov Sat Jul 20 12:19:00 1993 Message-Id: <199307202021.AA26628@oscsunb.ccl.net> Date: 20 Jul 93 16:19:00 EDT From: "STEPHEN R. HELLER" Subject: Internet contact person in Lisbon, Portugal To: "chemistry" I will be in Lisbon for a week in August at a meeting and want to connect to Internet. Does anyone have a contact in Lisbon for me to contact about a guest account for using e-mail. Thanx Steve Heller From adit@Kodak.COM Tue Jul 20 12:20:26 1993 Date: Tue, 20 Jul 93 16:20:26 EDT From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9307202020.AA00501@bcc9.kodak.com> To: chemistry@ccl.net Subject: Summary of docking refs. Folks, Sorry for the delay in summarizing for the net. Here is the table as I have it at present. Thanks to all for the help in getting it together. If anyone needs actual e-mail messages from which I extracted these refs I would be happy to send them out of course. The table is a bit wide. Sorry for the inconvenience. Adi. METHOD TRANS/ROT SMALL FLEXIBILITY MACRO FLEXIBILITY REF TORS ALL TERMS TORS ALL TERMS BROWNIAN DYNAMICS YES NO NO NO NO 2 SYSTEMATIC SEARCH NO YES NO NO NO 5 MONTE CARLO macromodel NO YES NO NO NO 1 ANNEALED DYNAMICS YES(?) (?) (?) (?) (?) 3 STERIC FITTING DOCK YES NO NO NO NO 4 MOLECULAR DYNAMICS YES(?) YES YES YES YES 8 MISCELLANEOUS HYBRID METHODS YES YES YES NO NO 6a NO YES YES(?) NO NO 6b,d,e YES YES YES YES YES 6c DISTANCE GEOMETRY YES YES YES(?) NO NO 7 REFERENCES: 1. W.C.Guida, R.S.Bohacek,M.D.Erion J.Compu.Chem. vol13, 214,(1992) 2.(a) S.A.Allison, S.H.Northrup, J.A.McCammon J.Chem.Phys., vol83 2894 (1985) (b) S.H.Northrup, H.P.Erickson Proc.Nat'l.Acad.Sci. vol89, 3338 (1992) 3. Goodsell,D.S. & Olson, A.J. (1990) Automnated Docking of Substrates to Proteins by Simulated Annealing. Proteins vol. 8, 195-202. 4. I.D. Kuntz; Science vol 257, pg 1078-1082 (1992) and refs cited therein. ## Full MD simulations to determine the entire docking process of a ligand to a macromolecule have not been reported to our knowledge. 5. D.Meyer, C.B.Naylor, I.Motoc, G.R.Marshall, J.Comput-Aided Mol. Des. vol1, 3 (1987) 6a. C.M.Freeman, C.R.A.Catlow, J.M.Thomas, S.Brode,Chem. Phys.Lett., 186, 137-142 (1991) 6b. Moon, J. B.; Howe, W. J. Tetrahedron Comp. Method. 1990, 3, 697-711. 6c. Gallion, S. and Ringe, D. (1992) Protein Engng. 5, 291-300. 6d. A.R. Leach et al; J.Comput.Chem. vol 13, pg 730-748 (1992) 6e. S.H.Rotstein, M.A.Murcko J.Comput-Aided Mol. Des. vol7, 23 (1993) 7. Blaney, J. M.; Dixon, J. S. Annual Reports in Medicinal Chemistry 1991, 26, 281-285. and references cited therein. 8.(a) B.L.Stoddard, D.E.Koshland Proc.Nat'l.Acad.Sci., vol90, 1146 (1993) and refs cited therein. (b) L.Banci, S.Schroder, P.A.Kollman, Proteins - Str. & Func. vol13, 288 (1992) NB: This list is not meant to be exhaustive. It is merely intended to illustrate the different strategies that have been used to dock small molecules into larger ones with some key refs for each.