From owner-chemistry@ccl.net Wed Feb 3 00:57:01 2010 From: "sitayya nandamuri sitayya-x-gmail.com" To: CCL Subject: CCL: CALCFC with ONIOM Message-Id: <-41169-100202151849-14658-4ckjb7FqCl7d0V3mq66nUQ!^!server.ccl.net> X-Original-From: "sitayya nandamuri" Date: Tue, 2 Feb 2010 15:18:45 -0500 Sent to CCL by: "sitayya nandamuri" [sitayya- -gmail.com] Is there a success for anyone of you folks when using CALCFC option iwht ONIOM computations. Whenever i used CALCFC with ONIOM, the job dies in the middle with THE FOLLOWING ERROR. I never understood whats going on ------------------------------------------------------------------------------ Leave Link 703 at Sat Jan 30 22:43:00 2010, MaxMem= 1879048192 cpu: 450.8 (Enter /usr/local/g09/g09/l716.exe) Dipole = 1.19280808D+01 5.19743678D-01 7.11141105D+00 Polarizability= 0.00000000D+00 0.00000000D+00 0.00000000D+00 0.00000000D+00 0.00000000D+00 0.00000000D+00 ***** Axes restored to original set ***** Operation on file out of range. FileIO: IOper= 1 IFilNo(1)= -585 Len= 89676 IPos= 0 Q=***************** dumping /fiocom/, unit = 1 NFiles = 93 SizExt = 524288 WInBlk = 2048 defal = T LstWrd = 4050065408 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 0 Base 41597339 41605120 68952064 41461760 40364032 78456832 55162880 68833280 End 41598976 41609216 76949504 41480192 40366080 88471552 66390016 68872192 End1 41598976 41609216 76949504 41480192 40366080 88471552 66390016 68872192 Wr Pntr 41597339 41605120 68952064 41461760 40364032 78456832 55162880 68833280 Rd Pntr 41597339 41605120 68952064 41461760 40364032 78456832 55162880 68833280 Length 1637 4096 7997440 18432 2048 10014720 11227136 38912 Number 0 0 0 0 0 0 0 0 Base 40472576 77090816 41613312 41482240 44062720 41070592 41592832 40409088 End 40476672 78387200 41615360 41492480 53850112 41457664 41596961 40413184 End1 40476672 78387200 41615360 41492480 53850112 41457664 41596961 40413184 Wr Pntr 40472576 77090816 41613312 41482240 44062720 41070592 41592832 40409088 Rd Pntr 40472576 77090816 41613312 41482240 44062720 41070592 41592832 40409088 Length 4096 1296384 2048 10240 9787392 387072 4129 4096 Number 0 501 502 503 507 508 511 514 Base 101496832 53248 40355840 198656 262144 90112 7942144 67526656 End 4050065408 54248 40360240 252891 340491 90142 8271412 67546159 End1 4050065408 55296 40361984 253952 342016 92160 8271872 67547136 Wr Pntr 101496832 53248 40355840 198656 262144 90112 7942144 67526656 Rd Pntr 101496832 53299 40355840 198656 340491 90112 7942957 67526656 Length 3948568576 1000 4400 54235 78347 30 329268 19503 Number 515 516 517 518 520 521 522 523 Base 67446784 40413184 67645440 67586048 41609216 40351744 41611264 41457664 End 67524796 40471693 68832562 67644557 41609226 40351779 41611658 41460434 End1 67526656 40472576 68833280 67645440 41611264 40353792 41613312 41461760 Wr Pntr 67446784 40413184 67645440 67586048 41609216 40351744 41611264 41457664 Rd Pntr 67446784 40413184 67645440 67586048 41609216 40351744 41611264 41457664 Length 78012 58509 1187122 58509 10 35 394 2770 Number 524 526 528 530 532 534 536 538 Base 68872192 76990464 68911104 76969984 76949504 77029376 77049856 77070336 End 68911001 77029273 68930607 76989487 76969007 77048879 77069359 77089839 End1 68911104 77029376 68931584 76990464 76969984 77049856 77070336 77090816 Wr Pntr 68872192 76990464 68911104 76969984 76949504 77029376 77049856 77070336 Rd Pntr 68872192 76990464 68911104 76969984 76949504 77029376 77049856 77070336 Length 38809 38809 19503 19503 19503 19503 19503 19503 Number 545 547 548 551 552 559 562 563 Base 41480192 78454784 41492480 38942720 47104 86016 38862848 40476672 End 41480220 78455178 41531289 38942758 47168 86018 38935182 40476869 End1 41482240 78456832 41531392 38944768 49152 88064 38936576 40478720 Wr Pntr 41480192 78454784 41492480 38942720 47104 86016 38862848 40476672 Rd Pntr 41480192 78454784 41492480 38942758 47168 86016 38862848 40476672 Length 28 394 38809 38 64 2 72334 197 Number 565 569 571 575 577 579 580 581 Base 40370176 78450688 78430208 1656832 88064 38936576 40361984 40366080 End 40370255 78450690 78449711 7941252 88116 38942602 40362394 40366341 End1 40372224 78452736 78450688 7942144 90112 38942720 40364032 40368128 Wr Pntr 40370176 78450688 78430208 1656832 88064 38936576 40361984 40366080 Rd Pntr 40370176 78450688 78430208 1656832 88064 38936576 40361984 40366080 Length 79 2 19503 6284420 52 6026 410 261 Number 582 583 584 585 588 590 598 603 Base 40368128 40478720 40372224 41596961 41533440 40484864 92160 68931584 End 40368719 40484747 40408380 41597339 41591949 41069954 92162 68951088 End1 40370176 40484864 40409088 41597339 41592832 41070592 94208 68952064 Wr Pntr 40368128 40478720 40408380 41596961 41533440 40484864 92160 68931584 Rd Pntr 40368128 40478720 40408380 41597339 41533440 40484864 92160 68931584 Length 591 6027 36156 378 58509 585090 2 19504 Number 605 606 607 619 634 665 670 674 Base 41598976 78428160 78452736 66390016 78387200 253952 40353792 342016 End 41605003 78428554 78452933 67257813 78428143 261246 40355516 396282 End1 41605120 78430208 78454784 67258368 78428160 262144 40355840 397312 Wr Pntr 41598976 78428160 78452736 66390016 78387200 253952 40353792 342016 Rd Pntr 41598976 78428160 78452736 67257813 78387200 258006 40355516 342016 Length 6027 394 197 867797 40943 7294 1724 54266 Number 679 680 685 687 691 694 695 698 Base 88471552 41615360 67547136 397312 39092224 41531392 67258368 38944768 End 101496646 44061271 67585945 1546170 40350898 41531786 67445202 38980924 End1 101496832 44062720 67586048 1546240 40351744 41533440 67446784 38981632 Wr Pntr 88471552 41615360 67547136 397312 39092224 41531392 67258368 38944768 Rd Pntr 88471552 41615360 67547136 397312 39092224 41531392 67258368 38980924 Length 13025094 2445911 38809 1148858 1258674 394 186834 36156 Number 700 701 742 989 991 992 993 994 Base 38981632 8271872 53850112 55296 77824 75776 51200 40960 End 39090184 38861549 55162337 75296 84386 75785 51400 40990 End1 39092224 38862848 55162880 75776 86016 77824 53248 43008 Wr Pntr 38981632 8271872 53850112 55296 77824 75776 51200 40960 Rd Pntr 38981632 8271872 53850112 55296 84386 75785 51400 40990 Length 108552 30589677 1312225 20000 6562 9 200 30 Number 995 996 997 998 999 Base 49152 45056 1546240 43008 94208 End 49172 45256 1654792 43208 196712 End1 51200 47104 1656832 45056 198656 Wr Pntr 49152 45056 1546240 43008 94208 Rd Pntr 49172 45256 1648763 43208 96712 Length 20 200 108552 200 102504 dumping /fiocom/, unit = 2 NFiles = 64 SizExt = 0 WInBlk = 2048 defal = F LstWrd = 88082432 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 0 Base 2984464 22215543 8001219 25955300 4157321 4284505 2584965 9421305 End 2987718 22219045 8007245 25961326 4175953 4284506 2600639 22213819 End1 2987718 22219045 8007245 25961326 4175953 4284506 2600639 22213819 Wr Pntr 2984464 22215543 8001219 25955300 4157321 4284505 2584965 9421305 Rd Pntr 2984464 22215543 8001219 25955300 4157321 4284505 2584965 9421305 Length 3254 3502 6026 6026 18632 1 15674 12792514 Number 0 0 501 502 503 508 511 520 Base 63530011 88081040 2987718 2600639 32300012 2486871 2604757 2961519 End 75055946 88082432 2988718 2604757 32354247 2486901 2934025 2961529 End1 75055946 88082432 2988718 2604757 32354247 2486901 2934025 2961529 Wr Pntr 63530011 88081040 2987718 2600639 32300012 2486871 2604757 2961519 Rd Pntr 63530011 88081040 2987718 2600639 32300012 2486871 2604757 2961519 Length 11525935 1392 1000 4118 54235 30 329268 10 Number 521 522 524 526 528 530 532 534 Base 2961631 2983873 4099009 9283044 4137818 2565462 2967710 2975711 End 2961666 2984267 4137818 9321853 4157321 2584965 2975711 2983712 End1 2961666 2984267 4137818 9321853 4157321 2584965 2975711 2983712 Wr Pntr 2961631 2983873 4099009 9283044 4137818 2565462 2967710 2975711 Rd Pntr 2961631 2983873 4099009 9283044 4137818 2565462 2967710 2975711 Length 35 394 38809 38809 19503 19503 8001 8001 Number 536 538 551 552 562 563 565 571 Base 9382299 9401802 2961593 2961529 2487101 2984267 2983712 9362796 End 9401802 9421305 2961631 2961593 2559435 2984464 2983721 9382299 End1 9401802 9421305 2961631 2961593 2559435 2984464 2983721 9382299 Wr Pntr 9382299 9401802 2961593 2961529 2487101 2984267 2983712 9362796 Rd Pntr 9382299 9401802 2961593 2961529 2487101 2984267 2983712 9362796 Length 19503 19503 38 64 72334 197 9 19503 Number 575 577 579 580 581 582 583 584 Base 25961326 2983821 2961666 2967692 2983721 2983794 2559435 2988718 End 32245746 2983873 2967692 2967710 2983794 2983821 2565462 3024874 End1 32245746 2983873 2967692 2967710 2983794 2983821 2565462 3024874 Wr Pntr 25961326 2983821 2961666 2967692 2983721 2983794 2559435 2988718 Rd Pntr 25961326 2983821 2961666 2967692 2983721 2983794 2559435 2988718 Length 6284420 52 6026 18 73 27 6027 36156 Number 603 605 619 634 665 670 674 675 Base 4079505 4284506 3024874 9321853 2934025 22213819 32245746 8007245 End 4099009 4284507 3892671 9362796 2941319 22215543 32300012 9283044 End1 4099009 4284507 3892671 9362796 2941319 22215543 32300012 9283044 Wr Pntr 4079505 4284506 3024874 9321853 2934025 22213819 32245746 8007245 Rd Pntr 4079505 4284506 3024874 9321853 2934025 22213819 32245746 8007245 Length 19504 1 867797 40943 7294 1724 54266 1275799 Number 676 677 678 679 680 687 695 698 Base 23515964 22219045 5433365 75055946 40960 4284507 3892671 32354247 End 25955300 23515964 8001219 88081040 2486871 5433365 4079505 32390403 End1 25955300 23515964 8001219 88081040 2486871 5433365 4079505 32390403 Wr Pntr 23515964 22219045 5433365 75055946 40960 4284507 3892671 32354247 Rd Pntr 23515964 22219045 5433365 75055946 40960 4284507 3892671 32354247 Length 2439336 1296919 2567854 13025094 2445911 1148858 186834 36156 Number 701 713 714 715 989 993 997 998 Base 32390403 62980080 62998164 63200665 2941319 2961319 4175953 2486901 End 62980080 62998164 63200665 63530011 2961319 2961519 4284505 2487101 End1 62980080 62998164 63200665 63530011 2961319 2961519 4284505 2487101 Wr Pntr 32390403 62980080 62998164 63200665 2941319 2961319 4175953 2486901 Rd Pntr 32390403 62980080 62998164 63200665 2941319 2961319 4175953 2486901 Length 30589677 18084 202501 329346 20000 200 108552 200 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 2048 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 40960 End 65536 End1 65536 Wr Pntr 40960 Rd Pntr 40960 Length 24576 Error termination in NtrErr: NtrErr Called from FileIO. ----------------------------------------------------------------------------------- I can quit using CALCFC option but without it the job is dying with link999 error which is because of shortage of cycles. Any help would be greatly appreciated. thanks in advance From owner-chemistry@ccl.net Wed Feb 3 01:32:01 2010 From: "David Sherrill sherrill(~)gatech.edu" To: CCL Subject: CCL: Georgia Tech Summer Theory Program 2010 Message-Id: <-41170-100202174103-32707-l5oLo9itXFejfOI0sVxG8w*o*server.ccl.net> X-Original-From: David Sherrill Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Tue, 2 Feb 2010 17:40:50 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: David Sherrill [sherrill^gatech.edu] Georgia Tech will host its annual Summer Theory Program as part of its NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 24 to July 30 and is open to students who will be in their junior or senior years during the next academic year. Theory students will work with Professors David Sherrill, Rigoberto Hernandez, Jean-Luc Bredas, or Angelo Bongiorno in the areas of electronic structure theory, nonequilibrium dynamics, electronic properties of materials, or DNA simulations. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $4500, a travel allowance, and housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html and http://www.chemistry.gatech.edu/undergraduate/summer/index.php The deadline for applications is February 15, 2010. -- C. David Sherrill, Ph.D. Professor School of Chemistry & Biochemistry School of Computational Science and Engineering Georgia Institute of Technology www.chemistry.gatech.edu/faculty/sherrill/ sherrill^gatech.edu, tel: 404-894-4037, fax: 404-894-7452 From owner-chemistry@ccl.net Wed Feb 3 08:46:00 2010 From: "Egon Willighagen egon.willighagen a gmail.com" To: CCL Subject: CCL: Call for Papers: Semantic Chemistry with the Resource Description Framework Message-Id: <-41171-100203080322-7609-vwfZl1HNQJqJYsgQ95bsMA]-[server.ccl.net> X-Original-From: Egon Willighagen Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Date: Wed, 3 Feb 2010 13:55:09 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egon.willighagen^^^gmail.com] 1st Call for Papers: Semantic Chemistry with the Resource Description Frame= work (CINF Symposium, ACS Autumn 2010) 240th ACS National Meeting & Exposition We now invite papers for our symposium on the use of the Resource Descripti= on Framework (RDF) technologies in semantic knowledge representation and data exchange in chemistry at the 240th National Meeting & Exposition of the Ame= rican Chemical Society (ACS) in Boston this fall. Semantic Chemistry has been around for a while, but is seeing a revival wit= h the adoption of the Resource Description Framework (RDF) and matching technologies in chemistry. RDF triples provide a simple structure that allo= w data and knowledge alike to be presented in a single framework. Derived technologies include the capturing of ontologies with the Web Ontology Language (OWL) and performing queries with SPARQL. A wide variety of free a= nd open source product make it easy to set up servers with large amounts of RD= F data, while integration with HTML is available too with RDFa. The RDF symposium at the 240th ACS national meeting in Boston invites submissions of talks about the use of RDF in chemistry and cheminformatics. Topics could include the use of OWL ontologies, OWL axioms, reasoning and interference, RDF in user interfaces, such as RDFa in web front ends, visualization, querying systems, and applications thereof, such as linking data sets, compound classification, cloud computing, web services, data aggregation, semantic publishing, and literature mining. Abstracts may be submitted via http://abstracts.acs.org. You=92ll find the RDF session as part of the CINF division symposiums. Submissions open Janua= ry 25, 2010, and the deadline is March 28, 2010. In case of questions, please = email Egon Willighagen at egon.willighagen*farmbio.uu.se or Martin Braendle at braendle*chem.ethz.ch. --=20 Post-doc * Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers From owner-chemistry@ccl.net Wed Feb 3 09:54:01 2010 From: "Ian Craig ianrcraig * gmail.com" To: CCL Subject: CCL: Papers using PCA to compare MD conformations to crystal structures? Message-Id: <-41172-100203094944-7104-5c75bLucz3YvDPJO1fT9qA]|[server.ccl.net> X-Original-From: "Ian Craig" Date: Wed, 3 Feb 2010 09:49:40 -0500 Sent to CCL by: "Ian Craig" [ianrcraig[*]gmail.com] Dear All, I am looking for papers in which Principal Component Analysis (or similar) is used to compare the protein conformations visited by an MD trajectory to a set of crystal (or NMR) structures. I imagine this must have been done in this past to characterize the extent of conformational sampling accomplished by MD simulations. However, I am having trouble tracking down firm examples. If anything springs to mind (even if it is just a name and a rough estimate of the year), I would greatly appreciate it. Regards, Ian. From owner-chemistry@ccl.net Wed Feb 3 12:12:01 2010 From: "Barry Hardy barry.hardy||vtxmail.ch" To: CCL Subject: CCL: eCheminfo Oxford 2010 Workshops - Bursary Awards, Case Studies Message-Id: <-41173-100203111541-8411-dptICmaajcF4SbQRZJHVMA:+:server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 03 Feb 2010 16:15:26 +0100 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy,vtxmail.ch] We will be holding the eCheminfo workshops in drug discovery and predictive ADME/tox again in Oxford this summer. In addition to exposure to a variety of methods, software and hands-on exercises, groups will work together on case studies throughout the workshop week. This year we will also include the potential to be involved in collaborative case studies supported by the Synergy project and running for several months before and after the workshop, including the potential to participate in the development and use of OpenTox web services in predictive toxicology (http://www.opentox.org/) The 5 day workshops take place in consecutive weeks end of July and beginning of August. Bursary Awards will be used to support the attendance of a selection of academic participants at the workshops. The deadline for submission is February 12. More Information at: http://barryhardy.blogs.com/cheminfostream/2010/02/bursary-award-applications-echeminfo-oxford-2010-workshops.html best regards Barry Hardy eCheminfo Community of Practice http://www.echeminfo.com/ Douglas Connect Switzerland From owner-chemistry@ccl.net Wed Feb 3 12:47:01 2010 From: "Basma Ghazal basmaghazal .. ymail.com" To: CCL Subject: CCL: BFGS method Message-Id: <-41174-100203091035-21003-nJwagJB1cFSjtRF49FTlVA%x%server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-1300524417-1265202949=:76831" Date: Wed, 3 Feb 2010 05:15:49 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal|,|ymail.com] --0-1300524417-1265202949=:76831 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable =C2=A0=0ADear CClers:=0AI want to begin my work on docking by redoing a pre= vious work. That uses BFGS method for the minimization of the compounds.=0A= I want to know what is the different between these method and SP4, TRIPOS, = MMFF94x and the other methods.=0AI will be highly appreciated if any one ex= plains this to me.=0ABest Regards,=0A=0A________________________________=0A= =0ABasma S. Ghazal=0AMSc. organic Chemistry =0A=E2=80=9CDrug design"=0A=C2= =A0Egypt.=0A=0A=0A --0-1300524417-1265202949=:76831 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A

 

=0A

Dear CClers:

=0A

I want to begin my work on do= cking by redoing a previous work. That uses = BFGS method for the minimization of the compounds.=

=0A

I want to know what is the different between these method and SP4, TRIPOS, MMFF94x and the other methods.=

=0A

I will be highly appreciated if any one explains t= his to me.

=0A

Best Regards,=

=0A
=0A
=0A
=0A

<= B>Basma S.= Ghazal
MSc. organic Chemistry

=0A

=E2=80=9CDrug design"<= /o:p>

=0A

 Egypt.

=0A


=0A= =0A --0-1300524417-1265202949=:76831-- From owner-chemistry@ccl.net Wed Feb 3 13:22:01 2010 From: "Omar Haq omar.haq_+_gmail.com" To: CCL Subject: CCL: Papers using PCA to compare MD conformations to crystal structures? Message-Id: <-41175-100203120820-15175-yRXYU5JebpNCIX28qZrMBw%a%server.ccl.net> X-Original-From: Omar Haq Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 3 Feb 2010 11:15:04 -0500 MIME-Version: 1.0 Sent to CCL by: Omar Haq [omar.haq]|[gmail.com] Try these papers from our group. They also might have relevant references that may be of interest to you. Paris, K.A., O. Haq, A.K. Felts, K. Das, E. Arnold, and R.M. Levy. Conformational Landscape of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Non-Nucleoside Inhibitor Binding Pocket: Lessons for Inhibitor Design from a Cluster Analysis of Many Crystal Structures. J. Med. Chem., 52, 6413-6420 (2009). Knight, J.L., Z. Zhou, E. Gallicchio, D.M. Himmel, R.A. Friesner, E. Arnold, and R.M. Levy. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion angle sampling. Acta. Cryst., D64, 383-396 (2008). Andrec, M., D.A. Snyder, Z. Zhou, J. Young, G.T. Montelione, and R.M. Levy. A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing. Proteins, 69, 449-465 (2007). Omar Haq Rutgers University On Wed, Feb 3, 2010 at 9:49 AM, Ian Craig ianrcraig * gmail.com wrote: > > Sent to CCL by: "Ian =A0Craig" [ianrcraig[*]gmail.com] > Dear All, > > I am looking for papers in which Principal Component Analysis (or similar= ) is used to compare the protein conformations visited by an MD trajectory = to a set of crystal (or NMR) structures. > > I imagine this must have been done in this past to characterize the exten= t of conformational sampling accomplished by MD simulations. However, I am = having trouble tracking down firm examples. > > If anything springs to mind (even if it is just a name and a rough estima= te of the year), I would greatly appreciate it. > > Regards, > > Ian. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 Omar From owner-chemistry@ccl.net Wed Feb 3 18:58:00 2010 From: "Kalju Kahn kalju#,#chem.ucsb.edu" To: CCL Subject: CCL: BFGS method Message-Id: <-41176-100203143628-5701-c16cNucpV4ro9HKO4ohh7A|a|server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 3 Feb 2010 10:59:40 -0800 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju#chem.ucsb.edu] Basma, BFGS is a minimization method that updates the Hessian (second derivative matrix) during the search using gradients (first derivative vectors). There is little bit of background on it at: http://www.chem.ucsb.edu/~kalju/chem126/public/minim_intro.html but you should really read the Broyden paper in J. Inst. Maths Applies (1970) 6, 222-231. SP4, TRIPOS, MMFF94 are force fields, e.g. analytical descriptions on how energy changes as a function of molecular geometry. You use BFGS as a search method to find a minimum of a molecule described by the TRIPOS or MMFF94 force field. Cheers, Kalju >   > Dear CClers: > I want to begin my work on docking by redoing a previous work. That uses > BFGS method for the minimization of the compounds. > I want to know what is the different between these method and SP4, TRIPOS, > MMFF94x and the other methods. > I will be highly appreciated if any one explains this to me. > Best Regards, > > ________________________________ > > Basma S. Ghazal > MSc. organic Chemistry > “Drug design" >  Egypt. > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Wed Feb 3 22:15:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim=compchem.net" To: CCL Subject: CCL: CALCFC with ONIOM Message-Id: <-41177-100203220007-30248-5dsmcS9Ycgl/xCm0IsNF1w*o*server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 3 Feb 2010 18:28:39 -0800 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim%x%compchem.net] Dear Sitayya Your error is not related to CALCFC keyword. Your error is related to a problem in calling the information from the checkpoint file. To solve it, you should check the following: * Checkpoint file's name is NOT using with other jobs. Sometimes, you may submit two jobs with the same checkpoint file name mistakenly. * You have enough space on your checkpoint file path. So, resubmit you job again using different checkpoint file's name and change it is path, make sure there is enough space on the new path. If you got the same error again, would you send me the input/output files? Sincerely. M. Ibrahim On 2/2/10, sitayya nandamuri sitayya-x-gmail.com wrote: > > Sent to CCL by: "sitayya nandamuri" [sitayya- -gmail.com] > Is there a success for anyone of you folks when using CALCFC option iwht ONIOM computations. > > Whenever i used CALCFC with ONIOM, the job dies in the middle with THE FOLLOWING ERROR. > > I never understood whats going on > ------------------------------------------------------------------------------ > Leave Link 703 at Sat Jan 30 22:43:00 2010, MaxMem= 1879048192 cpu: 450.8 > (Enter /usr/local/g09/g09/l716.exe) > Dipole = 1.19280808D+01 5.19743678D-01 7.11141105D+00 > Polarizability= 0.00000000D+00 0.00000000D+00 0.00000000D+00 > 0.00000000D+00 0.00000000D+00 0.00000000D+00 > ***** Axes restored to original set ***** > Operation on file out of range. > FileIO: IOper= 1 IFilNo(1)= -585 Len= 89676 IPos= 0 Q=***************** > > > dumping /fiocom/, unit = 1 NFiles = 93 SizExt = 524288 WInBlk = 2048 > defal = T LstWrd = 4050065408 FType=2 FMxFil=10000 > > Number 0 0 0 0 0 0 0 0 > Base 41597339 41605120 68952064 41461760 40364032 78456832 55162880 68833280 > End 41598976 41609216 76949504 41480192 40366080 88471552 66390016 68872192 > End1 41598976 41609216 76949504 41480192 40366080 88471552 66390016 68872192 > Wr Pntr 41597339 41605120 68952064 41461760 40364032 78456832 55162880 68833280 > Rd Pntr 41597339 41605120 68952064 41461760 40364032 78456832 55162880 68833280 > Length 1637 4096 7997440 18432 2048 10014720 11227136 38912 > > Number 0 0 0 0 0 0 0 0 > Base 40472576 77090816 41613312 41482240 44062720 41070592 41592832 40409088 > End 40476672 78387200 41615360 41492480 53850112 41457664 41596961 40413184 > End1 40476672 78387200 41615360 41492480 53850112 41457664 41596961 40413184 > Wr Pntr 40472576 77090816 41613312 41482240 44062720 41070592 41592832 40409088 > Rd Pntr 40472576 77090816 41613312 41482240 44062720 41070592 41592832 40409088 > Length 4096 1296384 2048 10240 9787392 387072 4129 4096 > > Number 0 501 502 503 507 508 511 514 > Base 101496832 53248 40355840 198656 262144 90112 7942144 67526656 > End 4050065408 54248 40360240 252891 340491 90142 8271412 67546159 > End1 4050065408 55296 40361984 253952 342016 92160 8271872 67547136 > Wr Pntr 101496832 53248 40355840 198656 262144 90112 7942144 67526656 > Rd Pntr 101496832 53299 40355840 198656 340491 90112 7942957 67526656 > Length 3948568576 1000 4400 54235 78347 30 329268 19503 > > Number 515 516 517 518 520 521 522 523 > Base 67446784 40413184 67645440 67586048 41609216 40351744 41611264 41457664 > End 67524796 40471693 68832562 67644557 41609226 40351779 41611658 41460434 > End1 67526656 40472576 68833280 67645440 41611264 40353792 41613312 41461760 > Wr Pntr 67446784 40413184 67645440 67586048 41609216 40351744 41611264 41457664 > Rd Pntr 67446784 40413184 67645440 67586048 41609216 40351744 41611264 41457664 > Length 78012 58509 1187122 58509 10 35 394 2770 > > Number 524 526 528 530 532 534 536 538 > Base 68872192 76990464 68911104 76969984 76949504 77029376 77049856 77070336 > End 68911001 77029273 68930607 76989487 76969007 77048879 77069359 77089839 > End1 68911104 77029376 68931584 76990464 76969984 77049856 77070336 77090816 > Wr Pntr 68872192 76990464 68911104 76969984 76949504 77029376 77049856 77070336 > Rd Pntr 68872192 76990464 68911104 76969984 76949504 77029376 77049856 77070336 > Length 38809 38809 19503 19503 19503 19503 19503 19503 > > Number 545 547 548 551 552 559 562 563 > Base 41480192 78454784 41492480 38942720 47104 86016 38862848 40476672 > End 41480220 78455178 41531289 38942758 47168 86018 38935182 40476869 > End1 41482240 78456832 41531392 38944768 49152 88064 38936576 40478720 > Wr Pntr 41480192 78454784 41492480 38942720 47104 86016 38862848 40476672 > Rd Pntr 41480192 78454784 41492480 38942758 47168 86016 38862848 40476672 > Length 28 394 38809 38 64 2 72334 197 > > Number 565 569 571 575 577 579 580 581 > Base 40370176 78450688 78430208 1656832 88064 38936576 40361984 40366080 > End 40370255 78450690 78449711 7941252 88116 38942602 40362394 40366341 > End1 40372224 78452736 78450688 7942144 90112 38942720 40364032 40368128 > Wr Pntr 40370176 78450688 78430208 1656832 88064 38936576 40361984 40366080 > Rd Pntr 40370176 78450688 78430208 1656832 88064 38936576 40361984 40366080 > Length 79 2 19503 6284420 52 6026 410 261 > > Number 582 583 584 585 588 590 598 603 > Base 40368128 40478720 40372224 41596961 41533440 40484864 92160 68931584 > End 40368719 40484747 40408380 41597339 41591949 41069954 92162 68951088 > End1 40370176 40484864 40409088 41597339 41592832 41070592 94208 68952064 > Wr Pntr 40368128 40478720 40408380 41596961 41533440 40484864 92160 68931584 > Rd Pntr 40368128 40478720 40408380 41597339 41533440 40484864 92160 68931584 > Length 591 6027 36156 378 58509 585090 2 19504 > > Number 605 606 607 619 634 665 670 674 > Base 41598976 78428160 78452736 66390016 78387200 253952 40353792 342016 > End 41605003 78428554 78452933 67257813 78428143 261246 40355516 396282 > End1 41605120 78430208 78454784 67258368 78428160 262144 40355840 397312 > Wr Pntr 41598976 78428160 78452736 66390016 78387200 253952 40353792 342016 > Rd Pntr 41598976 78428160 78452736 67257813 78387200 258006 40355516 342016 > Length 6027 394 197 867797 40943 7294 1724 54266 > > Number 679 680 685 687 691 694 695 698 > Base 88471552 41615360 67547136 397312 39092224 41531392 67258368 38944768 > End 101496646 44061271 67585945 1546170 40350898 41531786 67445202 38980924 > End1 101496832 44062720 67586048 1546240 40351744 41533440 67446784 38981632 > Wr Pntr 88471552 41615360 67547136 397312 39092224 41531392 67258368 38944768 > Rd Pntr 88471552 41615360 67547136 397312 39092224 41531392 67258368 38980924 > Length 13025094 2445911 38809 1148858 1258674 394 186834 36156 > > Number 700 701 742 989 991 992 993 994 > Base 38981632 8271872 53850112 55296 77824 75776 51200 40960 > End 39090184 38861549 55162337 75296 84386 75785 51400 40990 > End1 39092224 38862848 55162880 75776 86016 77824 53248 43008 > Wr Pntr 38981632 8271872 53850112 55296 77824 75776 51200 40960 > Rd Pntr 38981632 8271872 53850112 55296 84386 75785 51400 40990 > Length 108552 30589677 1312225 20000 6562 9 200 30 > > Number 995 996 997 998 999 > Base 49152 45056 1546240 43008 94208 > End 49172 45256 1654792 43208 196712 > End1 51200 47104 1656832 45056 198656 > Wr Pntr 49152 45056 1546240 43008 94208 > Rd Pntr 49172 45256 1648763 43208 96712 > Length 20 200 108552 200 102504 > > > dumping /fiocom/, unit = 2 NFiles = 64 SizExt = 0 WInBlk = 2048 > defal = F LstWrd = 88082432 FType=2 FMxFil=10000 > > Number 0 0 0 0 0 0 0 0 > Base 2984464 22215543 8001219 25955300 4157321 4284505 2584965 9421305 > End 2987718 22219045 8007245 25961326 4175953 4284506 2600639 22213819 > End1 2987718 22219045 8007245 25961326 4175953 4284506 2600639 22213819 > Wr Pntr 2984464 22215543 8001219 25955300 4157321 4284505 2584965 9421305 > Rd Pntr 2984464 22215543 8001219 25955300 4157321 4284505 2584965 9421305 > Length 3254 3502 6026 6026 18632 1 15674 12792514 > > Number 0 0 501 502 503 508 511 520 > Base 63530011 88081040 2987718 2600639 32300012 2486871 2604757 2961519 > End 75055946 88082432 2988718 2604757 32354247 2486901 2934025 2961529 > End1 75055946 88082432 2988718 2604757 32354247 2486901 2934025 2961529 > Wr Pntr 63530011 88081040 2987718 2600639 32300012 2486871 2604757 2961519 > Rd Pntr 63530011 88081040 2987718 2600639 32300012 2486871 2604757 2961519 > Length 11525935 1392 1000 4118 54235 30 329268 10 > > Number 521 522 524 526 528 530 532 534 > Base 2961631 2983873 4099009 9283044 4137818 2565462 2967710 2975711 > End 2961666 2984267 4137818 9321853 4157321 2584965 2975711 2983712 > End1 2961666 2984267 4137818 9321853 4157321 2584965 2975711 2983712 > Wr Pntr 2961631 2983873 4099009 9283044 4137818 2565462 2967710 2975711 > Rd Pntr 2961631 2983873 4099009 9283044 4137818 2565462 2967710 2975711 > Length 35 394 38809 38809 19503 19503 8001 8001 > > Number 536 538 551 552 562 563 565 571 > Base 9382299 9401802 2961593 2961529 2487101 2984267 2983712 9362796 > End 9401802 9421305 2961631 2961593 2559435 2984464 2983721 9382299 > End1 9401802 9421305 2961631 2961593 2559435 2984464 2983721 9382299 > Wr Pntr 9382299 9401802 2961593 2961529 2487101 2984267 2983712 9362796 > Rd Pntr 9382299 9401802 2961593 2961529 2487101 2984267 2983712 9362796 > Length 19503 19503 38 64 72334 197 9 19503 > > Number 575 577 579 580 581 582 583 584 > Base 25961326 2983821 2961666 2967692 2983721 2983794 2559435 2988718 > End 32245746 2983873 2967692 2967710 2983794 2983821 2565462 3024874 > End1 32245746 2983873 2967692 2967710 2983794 2983821 2565462 3024874 > Wr Pntr 25961326 2983821 2961666 2967692 2983721 2983794 2559435 2988718 > Rd Pntr 25961326 2983821 2961666 2967692 2983721 2983794 2559435 2988718 > Length 6284420 52 6026 18 73 27 6027 36156 > > Number 603 605 619 634 665 670 674 675 > Base 4079505 4284506 3024874 9321853 2934025 22213819 32245746 8007245 > End 4099009 4284507 3892671 9362796 2941319 22215543 32300012 9283044 > End1 4099009 4284507 3892671 9362796 2941319 22215543 32300012 9283044 > Wr Pntr 4079505 4284506 3024874 9321853 2934025 22213819 32245746 8007245 > Rd Pntr 4079505 4284506 3024874 9321853 2934025 22213819 32245746 8007245 > Length 19504 1 867797 40943 7294 1724 54266 1275799 > > Number 676 677 678 679 680 687 695 698 > Base 23515964 22219045 5433365 75055946 40960 4284507 3892671 32354247 > End 25955300 23515964 8001219 88081040 2486871 5433365 4079505 32390403 > End1 25955300 23515964 8001219 88081040 2486871 5433365 4079505 32390403 > Wr Pntr 23515964 22219045 5433365 75055946 40960 4284507 3892671 32354247 > Rd Pntr 23515964 22219045 5433365 75055946 40960 4284507 3892671 32354247 > Length 2439336 1296919 2567854 13025094 2445911 1148858 186834 36156 > > Number 701 713 714 715 989 993 997 998 > Base 32390403 62980080 62998164 63200665 2941319 2961319 4175953 2486901 > End 62980080 62998164 63200665 63530011 2961319 2961519 4284505 2487101 > End1 62980080 62998164 63200665 63530011 2961319 2961519 4284505 2487101 > Wr Pntr 32390403 62980080 62998164 63200665 2941319 2961319 4175953 2486901 > Rd Pntr 32390403 62980080 62998164 63200665 2941319 2961319 4175953 2486901 > Length 30589677 18084 202501 329346 20000 200 108552 200 > > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 2048 > defal = T LstWrd = 65536 FType=2 FMxFil=10000 > > Number 0 > Base 40960 > End 65536 > End1 65536 > Wr Pntr 40960 > Rd Pntr 40960 > Length 24576 > Error termination in NtrErr: > NtrErr Called from FileIO. > ----------------------------------------------------------------------------------- > I can quit using CALCFC option but without it the job is dying with link999 error which is because of shortage of cycles. > > > Any help would be greatly appreciated. > > thanks in advance> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim]=[compchem.net Website: www.compchem.net Fax No.: +20862342601 From owner-chemistry@ccl.net Wed Feb 3 22:50:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim|,|compchem.net" To: CCL Subject: CCL: BFGS method Message-Id: <-41178-100203221410-31379-l83xR0quMRdR1i/T7VXnyQ%server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Date: Wed, 3 Feb 2010 19:13:57 -0800 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim.:.compchem.net] Dear Basma BFGS (Broyden-Fletcher-Goldfarb-Shanno) is a pseudo Newton-Raphson Algorithm used to update Hassian matrix during geometry optimization. This method uses second derivate of energy to find the local minima, rather than Steepest and conjugate gradient methods which use first derivate of energy. SP4 (and SP5) is AMMP force filed, in which the force constants are calculated, not recalled from parameter files (bond length, bond angle and torsion angle files), and it's called atom oriented force filed. MM,Tripos,MMFF,AMBER,CHARMm,..etc are different force field parameterized against different molecules set and using different force field equations. Each one of these force fields is dominate for its parameterized set, for example, AMBER is working well for biological systems, MMFF is working well for the organic compounds. These force fields recall the force constant from parameters files (NOT compute it). Sincerely; M. Ibrahim On 2/3/10, Basma Ghazal basmaghazal .. ymail.com wrote: > > > > > > Dear CClers: > > I want to begin my work on docking by redoing a previous work. That uses > BFGS method for the minimization of the compounds. > > I want to know what is the different between these method and SP4, TRIPOS= , > MMFF94x and the other methods. > > I will be highly appreciated if any one explains this to me. > > Best Regards, > ________________________________ > > > Basma S. Ghazal > MSc. organic Chemistry > > =93Drug design" > > Egypt. > > > --=20 Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim{:}compchem.net Website: www.compchem.net Fax No.: +20862342601