From owner-chemistry@ccl.net Wed Jan 15 11:39:00 2014 From: "Hong-Guang Duan Hong-Guang.Duan_-_mpsd.cfel.de" To: CCL Subject: CCL:G: Gaussian failed when calculate large molecule Message-Id: <-49551-140115022620-14862-vw4mhAakbLGdBIhgBwc9Qg]_[server.ccl.net> X-Original-From: "Hong-Guang Duan" Date: Wed, 15 Jan 2014 02:26:19 -0500 Sent to CCL by: "Hong-Guang Duan" [Hong-Guang.Duan]~[mpsd.cfel.de] Hi, In those day, I use Gaussian calcualte large molecule, but it always failed when I try to use more complicated method and basis, like, B3LYP/6-31g(d). Idon't know the reason, but I think it caused by writting the large log.file. I use the personal computer. this is the com file and error information. #TD(Nstates=5) b3lyp/6-31g* pop=full density=current iop(9/40=9, 3/33=4) geom=connectivity Error: segmentation violation rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff rdx 0000000000000bc1, rsp 00007fffd37486c8, rbp 00007fffd3748ca0 rsi 000000000000000b, rdi 0000000000000bc1, r8 00002aecc1a37f40 r9 0000000000000000, r10 00007fffd3748460, r11 0000000000000202 r12 0000000000000000, r13 0000000000000000, r14 00007fffd3748ce8 r15 00007fffd374d060 --- traceback not available Aborted (core dumped) From owner-chemistry@ccl.net Wed Jan 15 12:14:01 2014 From: "Muhammad Jawad jawadfs[-]cemb.edu.pk" To: CCL Subject: CCL: ADMET properties by MOE Message-Id: <-49552-140115022825-14949-BPDopk7a6glXKkus3NwKAg^-^server.ccl.net> X-Original-From: "Muhammad Jawad" Date: Wed, 15 Jan 2014 02:28:24 -0500 Sent to CCL by: "Muhammad Jawad" [jawadfs{=}cemb.edu.pk] Dear all Please let me know, How to calculate descriptors for HIA (Human Intestinal Absorption), BBB (Blood Brain Barrier) penetration level, CYP450 inhibition , PPB and Hepatotoxicity using MOE, also if there is any freely available software or website? Looking for the information. Thanks in advance. Jawad jawadfs.^-^.cemb.edu.pk From owner-chemistry@ccl.net Wed Jan 15 12:49:00 2014 From: "Marcus Reitti moggen.reitti=-=gmail.com" To: CCL Subject: CCL: WFA-SAS request Message-Id: <-49553-140115044519-12416-P0GL1OO8xxROfCAbCpILZA=-=server.ccl.net> X-Original-From: "Marcus Reitti" Date: Wed, 15 Jan 2014 04:45:18 -0500 Sent to CCL by: "Marcus Reitti" [moggen.reitti]![gmail.com] Dear all, I am interested in obtaining the Wave Function Analysis - Surface Analysis Suite (WFA-SAS) by Dr. Felipe Bulat. It is available free of charge from Dr. Bulat directly, however the mail-address given at http://www.clevetheocomp.org/programs_and_resources_wfa_sas_screen.html seem to be offline. If anyone has access to the suite could you possibly share it with me? Sincerely, Marcus moggen.reitti_+_gmail.com From owner-chemistry@ccl.net Wed Jan 15 15:03:00 2014 From: "Jimmy Stewart MrMOPAC- -att.net" To: CCL Subject: CCL: MOPAC2012 modified to use GPU Message-Id: <-49554-140115143436-8775-ZizFqZ3Ok+6bTy2GfJrhzQ+*+server.ccl.net> X-Original-From: Jimmy Stewart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 15 Jan 2014 12:34:35 -0700 MIME-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC%att.net] MOPAC2012 has been modified to use Nvidia's GPU accelerator Prof. Rocha's group has modified MOPAC2012 to include CPU+GPU acceleration. This means that if a computer has a Nvidia GPU chip (Fermi or Kepler), and the CUDA Toolkit installed, then MOPAC2012 can use the GPU chip to reduce the computation time. Over the past year, Prof. Rocha's group has increased the speed of MOPAC2012 by a factor of about 200, for large systems. Thus for Bacteriorhodopsin, a medium-sized protein composed of 3352 atoms, the time for a single-point calculation, i.e., a 1SCF calculation, using a PC with four cores and one GPU chip, was reduced from 2,199 minutes for the legacy version of MOPAC2012 to 11.8 minutes. If a gradient calculation is included, the time rises to 13.4 minutes. This speed-up can be divided into three components: (1) By using Intel's MKL, legacy operations have been replaced by modern equivalents. This results in a speed-up of up to 42 times, for large systems. (2) By using Multi-Threading, a speed up of about three is achieved, when four threads are used, and about eight, when twelve threads are used. (3) For large systems, the use of a GPU chip approximately doubles the speed of a normal job. If you have a computer with a GPU chip installed, then please try the new MOPAC. Download Windows or Linux versions of MOPAC2012 that include in the label the letters "GPU". The CUDA toolkit, version 5.5 will need to be installed. Lastly, If you use any parallel version of MOPAC, please cite the following paper as a primary reference to MOPAC: Maia, J. D. C.; Urquiza Carvalho, G. A.; Mangueira, C. P.; Santana, S. R.; Cabral, L. A. F.; Rocha, G. B., Journal of Chemical Theory and Computation 2012, 8, 3072–3081. DOI: 10.1021/ct3004645. -- James J. P. Stewart Stewart Computational Chemistry 15210 Paddington Circle Colorado Springs CO 80921-2512 USA Tel: USA+(719) 488-9416 From owner-chemistry@ccl.net Wed Jan 15 16:32:00 2014 From: "Jim Kress ccl_nospam~!~kressworks.com" To: CCL Subject: CCL: WFA-SAS request Message-Id: <-49555-140115162921-27904-P/S2xJ4VZEM+XNPthtVRDQ(_)server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 15 Jan 2014 16:29:23 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam() kressworks.com] You can try through his LinkedIn profile: www.linkedin.com/in/felipebulat Jim -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com**ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com**ccl.net] On Behalf Of Marcus Reitti moggen.reitti=-=gmail.com Sent: Wednesday, January 15, 2014 4:45 AM To: Kress, Jim Subject: CCL: WFA-SAS request Sent to CCL by: "Marcus Reitti" [moggen.reitti]![gmail.com] Dear all, I am interested in obtaining the Wave Function Analysis - Surface Analysis Suite (WFA-SAS) by Dr. Felipe Bulat. It is available free of charge from Dr. Bulat directly, however the mail-address given at http://www.clevetheocomp.org/programs_and_resources_wfa_sas_screen.html seem to be offline. If anyone has access to the suite could you possibly share it with me? Sincerely, Marcus moggen.reitti[#]gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt