From chemistry-request@ccl.net Mon Mar 23 10:20:33 1992 Date: Mon, 23 Mar 92 09:56:36 GMT From: Mark Forster To: CHEMISTRY Status: R Subject: X-server issues. Dear Comp. Chemists. One additional thought on the X-server saga. When looking for a X-server (whether for a PC or other system) I feel the backing store facility is one of the most important features that you should seek. With backing store any window damage is repaired by copying the window contents from a memory buffer - this is quick. Without backing store the application program must detect any window damage events and issue graphics calls to redraw that window. This is OK if the image was cheap to compute - but if the image generation is compute bound then you will be stuck waiting for a very long redraw. The PC-XVIEW X-server does support backing store, this is also true of the X-server built by compiling the MIT release of X11 on a workstation (I did it on a SUN 3/160). Amazingly the server on the SGI Iris does not. They claim it's not required because the redraw is fast, but thats not true for a compute intensive image. If anyone at SGI is reading this I hope they implement backing store in a future IRIX release. Best Wishes Mark.Forster forster@comp.nibsc.ac.uk ps. sending message to CHEMISTRY%ccl.net@uk.ac.nsfnet-relay From chemistry-request@ccl.net Mon Mar 23 12:32:06 1992 Date: Mon, 23 Mar 1992 10:48 EST From: CHIRLIAN@CC.BRYNMAWR.EDU Subject: Batchmin using the GB/SA solvent model To: chemistry@ccl.net Status: R I have a question for anyone who is using BatchMin (part of MacroModel) to do Monte Carlo conformational searches using the GB/SA solvation model. When I reminimize the structures that are obtained in the Monte Carlo search, the energies _go up_ significantly (~12-13 kJ). The manual refers to a minor probelm invoving the effective radii which may result in larger gradients (but makes no mention of changes in energy) and suggests using the CHGF command to produce a charge file which can be used for subsequent minimizations. I have not been able to get this command to work, the output always includes the lines: CHG file not read, old charges retained and Charges come from force field. I am using the same command files as in the manual except I am using the MM2 force field rather than the OPLSA. I would appreciate hearing from anyone who has experience with these types of calculations. Specifically I would like to know if anyone else has had the energy rise when reminimizing structures (note: this only happens when solvent is included). If the energies rose, did writing out the .chg file solve the problem? How were you able to get the .chg file written, rather than having the charges read from the force field. Any insight would be appreciated. I am not concerned about the absolute energies, but would like to know if the ordering of structures can be trusted. I would also like to know why the energy _rises_. Thanks in advance for any help. Please e-mail any responses directly to me and I will summarize if there is sufficient interest. Lisa Chirlian From chemistry-request@ccl.net Mon Mar 23 15:17:16 1992 Date: Mon, 23 Mar 1992 10:43:12 PST From: kislin@SECS.UCSC.EDU Subject: Email address for Brookhaven PDB To: chemistry@ccl.net Status: R Howdy Folks: Does anyone have the address for the Brookhaven Protein Data Bank handy? Below is a pdb file for methanol. Can someone explain the data fields, specifically columns 5, 9 and 10. Is there an easy way to convert this data to the MDL molfile format? ATOM 1 C1 METH 1 3.875 0.678 -8.417 1.00 0.00 ATOM 2 1H1 METH 1 4.907 0.410 -8.516 1.00 0.00 ATOM 3 2H1 METH 1 3.406 0.026 -7.711 1.00 0.00 ATOM 4 3H1 METH 1 3.389 0.583 -9.366 1.00 0.00 ATOM 5 OH OHH 1B 3.774 2.028 -7.962 1.00 0.00 ATOM 6 HH OHH 1B 4.197 2.613 -8.596 1.00 0.00 TER Thanks in advance !! Brett S. Kislin Graduate Student UCSC Molecular Engineering Lab From chemistry-request@ccl.net Mon Mar 23 21:50:29 1992 Date: Mon, 23 Mar 92 18:08:01 PST From: whitbeck@wheeler.wrc.unr.EDU (Mike Whitbeck) Subject: address for journal To: chemistry@ccl.net Status: R If anyone has an address for an editor for Journal of Computers in/and Chemistry (??) I would appreciate it if you would e-mail it to me. If by chance an editor subscribes to the net I would appreciate some direct e-mail or a fax no. Many thanks in advance. Mike Whitbeck Desert Research Inst. whitbeck@wrc.unr.edu ................................................................... All academics have the potential for being insatiable... but the chemists are the most expensive and insatiable among the expensive and insatiable. - J. Martin in "To Rise Above Principle"