From owner-chemistry@ccl.net Fri Mar 17 01:03:00 2006 From: "FyD fyd===u-picardie.fr" To: CCL Subject: CCL: A review of force fields Message-Id: <-31222-060317010110-9320-oJDNZm1yIwwxLvXxTR0HOA---server.ccl.net> X-Original-From: FyD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 17 Mar 2006 07:00:53 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd(0)u-picardie.fr] Quoting "Ojwang, J.G.O. j.g.o.ojwang-.-tue.nl" : ],[ http://amber.scripps.edu/, you will find: An overview of the Amber protein force fields, and how they were developed, can be found in: J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001). regards, Francois > Sent to CCL by: "Ojwang, J.G.O." [j.g.o.ojwang**tue.nl] > > [the binary winmail.dat attachment removed by CCL admin] > > Good question! I'm also curious about the same especially in cases where > you have ionic or mixed ionic-covalent interactions. > > Regards to all. > > Ojwang' JGO > Eindhoven University of Technology. > > -----Original Message----- > From: Loan Huynh huynhkl2000**yahoo.ca [mailto:owner-chemistry##ccl.net] > Sent: Thu 3/16/2006 6:35 PM > To: Ojwang, J.G.O. > Cc: > Subject: CCL: A review of force fields > Sent to CCL by: Loan Huynh [huynhkl2000{:}yahoo.ca] > > > Hi All, > > I would like to gain knowlegde on force fields that are recently used > for the molecular dynamics. Does anyone know if there is a review on > the force field that are populated recently? From my understanding, > there is force field that is appropriate for macromolecular (i.e = > polymer), or force filed for protien, or small molecules ... > > Many thanks for your suggestions.0 > > LH. From owner-chemistry@ccl.net Fri Mar 17 07:12:00 2006 From: "Pablo Echenique Robba pnique]=[unizar.es" To: CCL Subject: CCL: Problems with Dalton 2.0 starting SCF guess Message-Id: <-31223-060317065806-30438-Fbx80C5mJa6X5Wl7w61t4Q^^server.ccl.net> X-Original-From: Pablo Echenique Robba Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 17 Mar 2006 12:10:55 +0100 MIME-Version: 1.0 Sent to CCL by: Pablo Echenique Robba [pnique%x%unizar.es] Dear everybody, I have some problems with Dalton 2.0. When I try to do an energy calculation at the HF level on the model dipeptide HCO-L-Ala-NH2, Dalton complains: WARNING: quantum number 4 not recognised for nucleus : 6 Hueckel start guess replaced with a diagonalization of H1 And refuses to use Hueckel guess (with .MOSTART EWMO he does the same). I really don't know what this warning means (even after reading the related FORTRAN source). I am 99% that my input molecule is properly formatted also. The problem is that, the refusal to do Hueckel produces non-convergence of the SCF iterations if large basis sets are used. So, my first question is: ¿What does this warning mean and how do I avoid it? The second thing is that I thought that maybe (I am not an expert in Quantum Chemistry), I may provide as an initial guess, the MO produced by a SCF calculation using a smaller basis set. So I run a 3-21G calculation and used the label .MOSTART NEWORB to input the file SIRIUS.RST in a 6-31++G(d,p) run. However, Dalton complains saying that the number of functions is different in the two basis sets and bombs out. So I guess that this is not the way. And my second question is: ¿Is there any way (in Dalton) for giving a smaller-basis-set calculation as a guess for a larger-basis-set calculation, instead of using Hueckel? Thanks everybody and regards, Pablo Echenique -- ------------------------------------ Pablo Echenique Robba Departamento de Fisica Teorica & Instituto de Biocomputacion y Fisica de los Sistemas Complejos BIFI Universidad de Zaragoza 50009 Zaragoza Spain Tel.: 34 976761260 E-mail: pnique(0)unizar.es ------------------------------------ From owner-chemistry@ccl.net Fri Mar 17 10:01:01 2006 From: "Andreas Heyden a.heyden|gmx.net" To: CCL Subject: CCL:G: Projected frequencies Message-Id: <-31224-060316105724-17748-zFSMSXi5lueLT8kpUE89Cw=-=server.ccl.net> X-Original-From: "Andreas Heyden" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 16 Mar 2006 15:57:05 +0100 (MET) MIME-Version: 1.0 Sent to CCL by: "Andreas Heyden" [a.heyden##gmx.net] Dear Ramon, Surprisingly, most program packages cannot calculate the for you appropriate hessian. There exist essentially two ways of calculating this reduced hessian matrix. 1.) Write your own small finite difference code to calculate the hessian matrix numerically. Next, make a frequency analysis as described in the one of the white papers from Gaussian. (Important do not project null-space out of your hessian matrix.) 2.) Put all your flexible atoms on top of your coordinate file and do a regular hessian calculation with your QM program package. Make sure that you use some kind of 'noproj' command so that you do NOT project out null-space after you hessian calculation which is usually the standard option. Carve out of your hessian the first 3Nflexible x 3Nflexible reduced hessian matrix and make a frequency analysis of this smaller hessian. Again the last part you have to programm by yourself. The first approach is probably better if the number of fixed atoms is significantly larger than the number of variable atoms or if your QM program has no analytical hessians. I personally programmed the second method for TURBOMOLE for one of my papers: J. Phys. Chem. B 2005, 109, 1857-1873. If you have any problems programming it by yourself, I can give you my code. Best regards, Andreas > --- Ursprüngliche Nachricht --- > Von: "Ramon Crehuet rcsqtc[a]iiqab.csic.es" > An: "Heyden, Andreas " > Betreff: CCL:G: Projected frequencies > Datum: Thu, 16 Mar 2006 08:38:04 -0500 > > Sent to CCL by: "Ramon Crehuet" [rcsqtc()iiqab.csic.es] > Dear CCLers, > I have a relatively large system where I keep some (external) atoms fixed. > After doing an optimisation I want to check that I have a minimum or a TS > candidate. So I would like to do a frequency calculation on the free atoms. > I think that makes sense from a theoretical point of view. So I do not > want to calculate the second derivative with respect to fixed atoms > coordinates, although they have to be there for the other derivatives to make sense. > Otherwise, I could get the full hessian and project it. > I was using gaussian and don't know how to do it with this software. Is > is possible? Is is possible with GAMESS-US (which I use regularly)? Is it > possible with any other software (that can also do DFT and ONIOM)? > And last, but not least... am I asking something very unusual? > Thanks in advance, > Ramon> > > -- Bis zu 70% Ihrer Onlinekosten sparen: GMX SmartSurfer! Kostenlos downloaden: http://www.gmx.net/de/go/smartsurfer From owner-chemistry@ccl.net Fri Mar 17 11:00:00 2006 From: "frisch{}gaussian.com (Michael Frisch)" To: CCL Subject: CCL:G: Projected frequencies Message-Id: <-31225-060317105835-801-5F98/mJlgqFMGxf349dedw\a/server.ccl.net> X-Original-From: frisch^gaussian.com (Michael Frisch) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 17 Mar 2006 10:57:00 -0500 Mime-Version: 1.0 Sent to CCL by: frisch],[gaussian.com (Michael Frisch) On Fri, Mar 17, 2006 at 10:25:04AM -0500, Andreas Heyden a.heyden|gmx.net wrote: > Sent to CCL by: "Andreas Heyden" [a.heyden##gmx.net] > > Dear Ramon, > > Surprisingly, most program packages cannot calculate the for you appropriate > hessian. There exist essentially two ways of calculating this reduced > hessian matrix. > 1. As some people have already noted, Gaussian 03 does do the proper projection of the frozen atoms during the vibrational frequency analysis if you mark the atoms as frozen in the input structure. 2. If you do analytic second derivatives with frozen atoms, then G03 does the same work as if no atoms were frozen. It should be smarter, but for now it isn't. 3. If you do numerical second derivatives, then G03 does differentiate only with respect to non-frozen atoms. So if just a few atoms are frozen, it is still better to do the analytic frequencies, but if most atoms are frozen then freq=numer may be preferable. Mike Frisch From owner-chemistry@ccl.net Fri Mar 17 12:53:00 2006 From: "Rzepa, Henry h.rzepa _ imperial.ac.uk" To: CCL Subject: CCL:G: ROHF/analytic Hessian and f,g,h functions? Message-Id: <-31226-060317124127-1288-AXyajigzB5AlKtdlLxt8ig-#-server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Fri, 17 Mar 2006 16:47:45 +0000 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa+/-imperial.ac.uk] Could anyone advise on what quantum codes support analytic 2nd derivatives for open shell ROHF wavefunctions with a basis which includes f functions and higher? G03 does not do this ; GAMESS(US) does so only for bases without f and higher, Jaguar does not. Before trying the rest of the breed, I thought I might ask this list? -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs%x%mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Fri Mar 17 13:28:01 2006 From: "Cory Pye cpye|a|crux.smu.ca" To: CCL Subject: CCL: Problems with Dalton 2.0 starting SCF guess Message-Id: <-31227-060317132538-20708-EjjkVOMaJJhYl8vZB4KiOw**server.ccl.net> X-Original-From: Cory Pye Content-Transfer-Encoding: 8bit Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Date: Fri, 17 Mar 2006 14:25:32 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye%%crux.smu.ca] Hello, Could it be that one of your atoms is being misinterpreted? For example, your system contains H, C, N, and O. Some programs differentiate atom labels by using something like H1 or H2. If you decided to use a letter to distinguish a hydrogen, e.x. HA, HB, ... then HE would be misinterpreted as helium, HF as hafnium, etc. CA should be carbon A, but could be treated as calcium, CD as cadmium, etc. Some of these elements are pretty deep in the periodic table and wouldn't have defined Huckel parameters, forcing it to diagonalize the core Hamiltonian (H1?). Check the atomic numbers to make sure they are correct. I used a different sized basis set guess in GAMESS once. I wrote a little F77 program to read in the PUNCH file, append 0's where necessary, and then rewrite the matrix in the same format. If the basis set is ordered similarly in the program, it works, or one can use a suitable indexing function. You could probably use awk or perl to do the same thing. -Cory On Fri, 17 Mar 2006, Pablo Echenique Robba pnique]=[unizar.es wrote: > Sent to CCL by: Pablo Echenique Robba [pnique%x%unizar.es] > Dear everybody, > I have some problems with Dalton 2.0. When I try to do an energy > calculation at the HF level on the model dipeptide HCO-L-Ala-NH2, Dalton > complains: > > WARNING: quantum number 4 not recognised for nucleus : 6 > Hueckel start guess replaced with a diagonalization of H1 > > And refuses to use Hueckel guess (with .MOSTART EWMO he does the > same). I really don't know what this warning means (even after reading > the related FORTRAN source). I am 99% that my input molecule is properly > formatted also. > The problem is that, the refusal to do Hueckel produces > non-convergence of the SCF iterations if large basis sets are used. > So, my first question is: > > ¿What does this warning mean and how do I avoid it? > > The second thing is that I thought that maybe (I am not an expert in > Quantum Chemistry), I may provide as an initial guess, the MO produced > by a SCF calculation using a smaller basis set. So I run a 3-21G > calculation and used the label .MOSTART NEWORB to input the file > SIRIUS.RST in a 6-31++G(d,p) run. However, Dalton complains saying that > the number of functions is different in the two basis sets and bombs out. > So I guess that this is not the way. And my second question is: > > ¿Is there any way (in Dalton) for giving a smaller-basis-set > calculation as a guess for a larger-basis-set calculation, instead of > using Hueckel? > > Thanks everybody and regards, > > Pablo Echenique > > -- > > ------------------------------------ > Pablo Echenique Robba > > Departamento de Fisica Teorica > & > Instituto de Biocomputacion y > Fisica de los Sistemas Complejos > BIFI > > Universidad de Zaragoza > 50009 Zaragoza > Spain > > Tel.: 34 976761260 > E-mail: pnique|unizar.es > ------------------------------------> > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye{:}crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Fri Mar 17 14:27:00 2006 From: "Andrew Good Andrew.Good,+,bms.com" To: CCL Subject: CCL: 5 $1150 CCG Excellence Student Travel Award Stipends Available for the, Fall San Francisco ACS Message-Id: <-31228-060317134611-1916-AcJCaCmy4helDCNvbp/iBw]~[server.ccl.net> X-Original-From: Andrew Good Content-return: prohibited Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=us-ascii Date: Fri, 17 Mar 2006 13:42:33 -0500 MIME-version: 1.0 Sent to CCL by: Andrew Good [Andrew.Good*o*bms.com] 5 $1150 CCG Excellence Student Travel Award Stipends Available for the Fall San Francisco ACS: The CCG Excellence Awards have been created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are gradute students of the Americas in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. For details of application requirments visit the CCG Award url at http://membership.acs.org/C/COMP/CCG/ccg.html Note: Closing date for submissions is Apr 25 2006. From owner-chemistry@ccl.net Fri Mar 17 15:01:00 2006 From: "Darryl Reid darryl.reid(_)gmail.com" To: CCL Subject: CCL: How to choose a docking program? Message-Id: <-31229-060317114231-26147-TCDVjqNv/vJGQ0w4TJqoFw,+,server.ccl.net> X-Original-From: "Darryl Reid" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 17 Mar 2006 10:38:49 -0500 MIME-Version: 1.0 Sent to CCL by: "Darryl Reid" [darryl.reid**gmail.com] SimBioSys has a whitepaper on eHiTS that gives an overview of docking in general, you may wish to take a look at that. http://www.simbiosys.ca/solutions/white_papers/eHiTS_Whitepaper.pdf Darryl On 3/15/06, Jianxi Xiao jianxix ~~ eden.rutgers.edu wrote: > Sent to CCL by: "Jianxi Xiao" [jianxix[-]eden.rutgers.edu] > Hi, CCLers, > > I am trying to dock a small DNA (~22nt) to a large protein (~ 770 residues) based on the known structures. I have no experience about docking, and there are so many docking proprams like autoDock, Dock, Sybyl, MONTY. Which one should I choose? Thanks a lot! > > Jianxi Xiao > Rutgers University > Department of Chemistry > 610 Taylor Rd > Piscataway, NJ 08854 > jianxix[a]eden.rutgers.edu> > > > From owner-chemistry@ccl.net Fri Mar 17 15:36:00 2006 From: "Marco Parenti mdparenti\a/unimo.it" To: CCL Subject: CCL: Training course schedule spring-summer 2006 Message-Id: <-31230-060317113831-24573-iy2iebYC1nhQ5dP7TPRPiQ-#-server.ccl.net> X-Original-From: "Marco Parenti" Date: Fri, 17 Mar 2006 11:38:27 -0500 Sent to CCL by: "Marco Parenti" [mdparenti|,|unimo.it] S-IN Soluzioni Informatiche (www.s-in.it) is pleased to announce the course calendar for spring-summer 2006; Courses organized in partnership with Umetrics: Design of experiment and optimisation May 10-12 Deadline for subscription: April 19 Multivariate Data Analysis May 17-19 Deadline for subscription: April 26 Courses organized by S-IN: Quantum Mechanics: Applications to Organic Chemistry and Molecular Modelling May 25-26 Deadline for subscription: May 4 Molecular Mechanics: Applications to Organic Chemistry and Molecular Modelling June 6-7 Deadline for subscription: May 16 Molecular Mechanics: Advanced course June 8-9 Deadline for subscription: May 18 Basics of Protein Sequence Analysis June 13-14 Deadline for subscription: May 23 All courses will take place in Vicenza (Italy); the official language will be Italian. The courses will include both lectures and practical exercises. For full Course Descriptions and Registration Information: www.s-in.it or mail to info ~~ s-in.it. From owner-chemistry@ccl.net Fri Mar 17 16:11:00 2006 From: "David A. Case case**scripps.edu" To: CCL Subject: CCL: How to choose a docking program? Message-Id: <-31231-060316195634-22594-Nhfj0TOPKwmJ37usGVcJzQ^-^server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 16 Mar 2006 16:19:13 -0800 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case(!)scripps.edu] On Wed, Mar 15, 2006, Jianxi Xiao jianxix ~~ eden.rutgers.edu wrote: > > I am trying to dock a small DNA (~22nt) to a large protein (~ 770 residues) > based on the known structures. I have no experience about docking, and there > are so many docking proprams like autoDock, Dock, Sybyl, MONTY. Which one > should I choose? Thanks a lot! > The "DOT" program has a reasonably good ability to find potential DNA/protein conformations at the size range you are talking about. But you have to add human intervention as well: it doesn't give just one answer, but a (ranked) series of possibilities. Generally, it is important to cluster those and look for regularities. As a minimal example, change the DNA position by one full turn of helix generally yields a related possible structure. The bottom line is that you have to learn how to interpret the results. Since you have no experience, be prepared to spend some time and effort to get useful results: this is not a simple or solved problem. For examples, see this paper: %A V.A. Roberts %A D.A. Case %A V. Tsui %T Predicting Interactions of Winged-Helix Transcription Factors with DNA %J Proteins %V 57 %P 172-187 %D 2004 ....dave case From owner-chemistry@ccl.net Fri Mar 17 16:47:02 2006 From: "Steve Williams willsd=-=appstate.edu" To: CCL Subject: CCL:G: ROHF/analytic Hessian and f,g,h functions? Message-Id: <-31232-060317151520-19193-6VaKNjO+mBvtKqrvAnBakA,,server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Fri, 17 Mar 2006 13:54:17 -0500 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd%appstate.edu] Rzepa, Henry h.rzepa _ imperial.ac.uk wrote: >Sent to CCL by: "Rzepa, Henry" [h.rzepa+/-imperial.ac.uk] >Could anyone advise on what quantum codes support analytic 2nd derivatives >for open shell ROHF wavefunctions with a basis which includes f functions >and higher? > >G03 does not do this ; GAMESS(US) does so only for bases without >f and higher, Jaguar does not. Before trying the rest of the breed, >I thought I might ask this list? > > The manual for ACESII indicates that it has analytic Hessians for ROHF models, but it does not specifically include or exclude any basis sets for that (or for any other) methods. The qchem manual says that qchem has analytic Hessians with f orbitals for hf, dft, and cis. It does not specifically refer to rohf except to say that analytic gradients and Hessians are NOT availabe for cis with ro. Steve Williams From owner-chemistry@ccl.net Fri Mar 17 17:21:00 2006 From: "Jose Gascon jose.gascon##yale.edu" To: CCL Subject: CCL:G: ONIOM Convergence Message-Id: <-31233-060317155348-8505-c7QS/mImtPmBxmPzNWNOgg**server.ccl.net> X-Original-From: Jose Gascon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 17 Mar 2006 15:00:32 -0500 MIME-Version: 1.0 Sent to CCL by: Jose Gascon [jose.gascon++yale.edu] My suggestion is to try first (hf/3-21g:amber). If you get this to converge then increase the level of theory and then the basis set, or vice versa. With respect to using PM3, I've seen before this type of problems with g03, so it might be an intrinsic problem of the semi-empirical gradients implementation in g03. Another possible problem, make sure you have all van der waals parameters defined in the oniom input file for atoms that are not parametrized in the Amber force field. Jose. -- Jose A. Gascon - Postdoctoral Associate http://xbeams.chem.yale.edu/~batista/jose/Jose.html Department of Chemistry - (203)432-5911; jose.gascon .. yale.edu Yale University P.O. Box 208107 New Haven, CT 06520-8107. From owner-chemistry@ccl.net Fri Mar 17 17:57:01 2006 From: "Niels Johan Christensen njc(!)kvl.dk" To: CCL Subject: CCL: Problems Running MORPHY 1.0 on a Redhat Enterprise Linux system. Message-Id: <-31234-060317061557-19085-wgZPtHY7jYzJplxDEnHL8A:+:server.ccl.net> X-Original-From: "Niels Johan Christensen" Date: Fri, 17 Mar 2006 06:15:56 -0500 Sent to CCL by: "Niels Johan Christensen" [njc=kvl.dk] Dear All. I have obtained MORPHY 1.0 from the Computer Physics Communcations Program Library. While it is possible for me to compile the program(s) on a Redhat Enterprise Linux 4 (EM64T) system, MORPHY error terminates when I try to run the test1 and test2 examples. I assume that the reported error (see MORPHY output below) may be due to my choice of an unsupported platform (i.e. linux). Any help is highly appreciated. Thanks in advance. Best regards, Niels Johan Christensen ALLINIT starts ALLINIT ends INPUT starts INPUTOUTT starts INPUTOUTT ends INPUTWAVE starts INPUTWAVE done INPUTSHOW starts INPUTSHOW ends INPUTPLOT starts INPUTPLOT ends INPUTFEED starts INPUTFEED ends INPUTPROP starts INPUTPROP ends INPUTFITT starts invalid integer: read unexpected character apparent state: unit 11 named test1.inp last format: list io lately reading sequential formatted external IO Aborted