From jkl@ccl.net Thu Oct 10 10:11:14 1991 Date: Thu, 10 Oct 91 10:11:10 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: Re: Bug in Mopac ESP code fixed Status: R I (jkl@ccl.net) am forwarding this message to the list ---------- Begin Forwarded Message ---------- >From bbesler@ouchem.chem.oakland.edu Thu Oct 10 07:04:15 1991 Date: Thu, 10 Oct 91 07:05:53 -0400 From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) To: chemistry-request@ccl.net Subject: Bug in Mopac ESP code fixed Status: R There is a bug in the subroutine elesp of Mopac 5.0 ESP and the ESP code in Mopac 6.0. In Mopac 6.0 all of the ESP code is in the esp.rof file which gets renamed and compiled if the ESP code is desired. The bug is that the z cartesian coordinates being written to unit 21 were in BOHR whereas the x and y coordinate were in agnstroms which is what the should be. The bug is fixed in the download versions on ouchem.chem.oakland.edu(141.210.108.5). If you have Mopac 5.0 ESP download just the file elesp.f and if you have Mopac 6 download esp.rof from either the vax or unix directories. ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Thu Oct 10 11:08:23 1991 Date: Thu, 10 Oct 91 09:49:09 EST From: Shaun Black Subject: TER Statements in PDB Files To: "Scott Le Grand et al." Status: R Dear Scott et al., The TER statement in a PDB file signals the end of a protein chain. There can be zero or more TER's in a file. The syntax is: TER entrynumber residuename chainchar residuenumber where 'entrynumber' is the entry number of the file following the C -terminus of the given peptide chain, 'residuename' is the C-terminus of the given chain, 'chainchar' (optional if only one chain) is the designator for the given chain, and 'residuenumber' is the residue number of the C-terminus of the given chain. For example, as found in "1TNF": TER 3681 LEU C 157 However, as you might have noticed, the use of the TER command is rather heterogeneous. For example, "1DHF" has a single chain and uses no TER after the C-terminus (Asn 185) and before HETATM's for the folate cofactor and defined water, whereas "2LIV" has only one chain but uses a TER after the C-terminus (Lys 344) and before the defined HETATM waters. "1FCB" uses TER's after each C-terminus and before all HETATM's associated with each chain. Personally, I feel it is best always to use the TER statement; problems associated with file compatibility will be minimized. Hope this is helpful. -Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= - Shaun D. Black, PhD | Bitnet: black@ohstphrm.bitnet - = Ohio State University | Internet: black@ohstphrm.pharmacy.ohio-state.edu = - College of Pharmacy | Phone: (614) 292-3925 - = 500 West 12th Avenue | FAX: (614) 292-2435 = - Columbus, OH 43210-1291 | :-) (...Start every day with a smile...) - =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Thu Oct 10 12:02:43 1991 Date: Thu, 10 Oct 91 16:42:52 CET From: dufner@ws05.pc.chemie.th-darmstadt.de (Hagen Dufner) To: chemistry@ccl.net Subject: RE: ewald summation Status: R Hi folks, can anybody tell me where I get a programm (C or Fortran) to do rapid Ewald summations Thanks +---------------------------------------+-----------------------------------+ | Hagen Dufner | TH Darmstadt, PC I | | | Petersenstr 20 | | Ab initio calculations on Zeolites | 6100 Darmstadt, FRG | | | Phone: (+int) 6151 162798 | | | Fax: (+int) 6151 164298 | +---------------------------------------+-----------------------------------+ | Network : | | | +---------------------------------------------------------------------------+ From chemistry-request@ccl.net Thu Oct 10 12:50:21 1991 Date: Thu, 10 Oct 91 12:25:34 EDT From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: Scratch space requirement for Gauss86 To: chemistry@ccl.net Status: R Hello, I've just subscribed to this list/newsgroup. I'm a computer programmer who installed the NEC version of Gaussian86 on the NEC SX-1A Supercomputer. I'm now 'supporting' the software, but I know next to nothing about computational chemistry. The problem: G86 on the SX uses a tremendous amount of scratch filespace for the INTEGRAL and RWF (readwrite) files. Both these files are 'direct access' files whose sizes need to be 'allocated' before execution of the job. And there is no 'file expansion' facility. Most of the time, users just allocate a large scratch space without really knowing how much they actually need. If the space is insufficient, the program aborts (after much wasted cpu hrs). Question: Is there a way to calculate beforehand, the size of the INTEGRAL and RWF files, given the input to the G86 program? It would be most appreciated if anyone could provide some answers or suggestions. A user is currently trying to run a G86 job on the SX with 450MBytes of integral file space and 700MBytes of readwrite file space. And this is NOT enough!!! The program aborted due to insufficient filespace for the readwrite file. Another question is: Is this sort of filesize for the integrals and readwrite file typical?? I'm at a loss as to how to secure more disk space. Thanks in advance for any response. Heng Kek Analyst Programmer Computer Centre National University of Singapore Acknowledge-To: It is common for ab initio calculations to use large amounts of disk space. The current version of Gaussian can trade CPU time for disk space for the most common types of calculation (Hartree-Fock and MP2), and is much, much faster, but these capabilities were not present in Gaussian 86. The integral file size depends on the number of basis functions. It will be roughly 1.5N^4 bytes or 2N^4 bytes long, depending on how the integral labels are packed (whether they fill 32 or 64 bits). For open-shell Hartree-Fock calculations, the size will be 2.5N^4 or 3N^4. The read-write file size depends on N^2 for Hartree-Fock calculations, and on N^4 in a complicated way for post-SCF calculations. The easiest way to estimate the size is to run a smaller job an scale the size by the ratio of OV^3 for the jobs (O=number of electrons, V=N-O=number of virtuals). The limitation of not being able to extend these files is specific to the NEC implementation of Gaussian and is not present on other versions. Contact your NEC representative for an explanation. All this is for Gaussian 86, of course. For SCF and MP2 calculations in Gaussian 90 the integral file isn't needed. For MP2, whatever disk is made available for the read-write file is used, with quantities being recomputed instead of trying to use more disk than there is. Michael Frisch Gaussian, Inc. ------- From chemistry-request@ccl.net Thu Oct 10 23:21:51 1991 Date: Fri, 11 Oct 91 10:45:17 SST From: Heng Kek Subject: Indications of INT and RWF file sizes in output of Gauss86? To: Computational Chem Grp at Ohio Supercom Ctr Status: R Hello, It's me again, the non-Quantum chemistry person. I would like to know if the output of G86 gives any indication of the amount of disk space it used for the INT and RWF files? If it does, then where do I look or how do I get the figure? If it doesn't, then I would never know if my estimation of the file sizes needed were accurate or not. I'm running Gaussian 86 on the NEC SX1A supercomputer. Any comments and answers would be most appreciated. Heng Kek Analyst Programmer Computer Centre National University of Singapore