From owner-chemistry@ccl.net Fri Apr 20 02:25:01 2007 From: "sriram boppana sri.boppana%%gmail.com" To: CCL Subject: CCL: how to interpret Fred docking scores Message-Id: <-34079-070420022207-20923-oFKsG/REuSfGfWurLNId+w[a]server.ccl.net> X-Original-From: "sriram boppana" Date: Fri, 20 Apr 2007 02:22:03 -0400 Sent to CCL by: "sriram boppana" [sri.boppana#gmail.com] Hi All Does any one knows to how to interpret docking results of FRED(openeye)what is best score and what is least score. the out put file shows in -ve valuse. It would be very helpful if someone could Explain. Thanks Sri From owner-chemistry@ccl.net Fri Apr 20 03:00:01 2007 From: "Martin Mueller martin.mueller|*|ime.fraunhofer.de" To: CCL Subject: CCL: mol converters Message-Id: <-34080-070419144054-25434-vT9UqPQ0dFwthJqJeFZvaw/./server.ccl.net> X-Original-From: Martin Mueller Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Apr 2007 17:24:42 +0200 MIME-Version: 1.0 Sent to CCL by: Martin Mueller [martin.mueller[a]ime.fraunhofer.de] Hi, I'm looking for convertes for chemical structures. (mol to smiles, mol to xyz etc.) I found: ChemAxons molconverter http://www.chemaxon.com/product/molcon.html which is free for academic use only Open Babel http://openbabel.sourceforge.net/wiki/Main_Page which seems to be "free" (GPL) ACD/Chemsketch http://www.acdlabs.com/download/chemsk.html Any other available? Martin From owner-chemistry@ccl.net Fri Apr 20 03:34:01 2007 From: "Martin Mueller martin.mueller(0)ime.fraunhofer.de" To: CCL Subject: CCL: summary: chemical database software Message-Id: <-34081-070419111248-5174-MnlCbBV028zsJo19gypwMA(a)server.ccl.net> X-Original-From: Martin Mueller Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Apr 2007 12:37:50 +0200 MIME-Version: 1.0 Sent to CCL by: Martin Mueller [martin.mueller,ime.fraunhofer.de] Hi, some weeks ago I asked for chemical database software. Instead of copying all answers, I simply will give pointers to the solutions which where reported or found by google. Hints for other systems are appreciated! Martin --------- List of pointers.... Cambridgesoft: http://www.cambridgesoft.com/solutions/details/?es=2 gNova: http://www.gnova.com/ Daylight: http://www.daylight.com/products/daycart.html Chemaxon: http://www.chemaxon.com/product/jc_base.html http://www.chemaxon.com/product/jc_cart.html Molsoft: http://www.molsoft.com/molcart.html Bio-rad: http://www.bio-rad.com MDL Isentris: http://www.mdl.com/products/framework/isentris/ Infochem: http://www.infochem.de/en/products/software/iccartridge.shtml From owner-chemistry@ccl.net Fri Apr 20 04:09:01 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas^-^chem.elte.hu" To: CCL Subject: CCL:G: Basis sets for ONIOM in G03 Message-Id: <-34082-070420033446-26867-PSdynCfptnDCkWeF/srY3A],[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 20 Apr 2007 09:32:13 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas_-_chem.elte.hu] Hi Rich, Yes, it is POSSIBLE to use DFT or any other implemented method at any level. However, Morokuma used to note in his lectures that DFT SHOULD NOT be used as medium or low level in ONIOM because its error is not systematic, therefore, may cause large error in the extrapolation scheme. Using DFT for the high level should be fine. The "GenECP for ONIOM" part of your question was already addressed on CCL and seems that the only solution is using the "External" keyword and set it up for Gaussian external call (might need some script programing). Best wishes, Ödön On Thu, 2007-04-19 at 23:27 -0400, Richard Huhn huhnra^^mit.edu wrote: > Sent to CCL by: "Richard Huhn" [huhnra-$-mit.edu] > I am using Gaussian 03 to do ONIOM calculations of some very large molecules containing transition metals. I have a two-part question: > > Is it possible to use two DFT methods in an ONIOM calculation? For example, the high level could use a different functional than the lower level(s); or, the high level could use a larger basis set than the lower level(s). > > If either of these cases are possible, how does one input a general basis set (as with the GenECP keyword) that will supply the different basis sets for the different levels? This problem is not encountered in the examples in the G03 manual, in which only MM or semi-empirical methods are used as the low layer. An example of a working input file would be greatly helpful. Thank you for any help or pointers! > > Rich Huhn> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Fri Apr 20 06:25:04 2007 From: "Szabolcs Csepregi scsepregi-.-chemaxon.com" To: CCL Subject: CCL: mol converters Message-Id: <-34083-070420051408-26755-59a5THnHrrIeHiZjy7dtDg[-]server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Apr 2007 11:13:54 +0200 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi[#]chemaxon.com] Hi Martin, Just a small clarification: MolConverter is free for everyone, if not used as integral parts of other applications. See: http://www.chemaxon.com/prices.html Cheers, Szabolcs Szabolcs Csepregi, PhD Director of Search Technologies, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 > Sent to CCL by: Martin Mueller [martin.mueller[a]ime.fraunhofer.de] > > ChemAxons molconverter > http://www.chemaxon.com/product/molcon.html > which is free for academic use only From owner-chemistry@ccl.net Fri Apr 20 06:31:00 2007 From: "Tamas Gunda tgunda2:-:puma.unideb.hu" To: CCL Subject: CCL: mol converters Message-Id: <-34084-070420062040-1609-1e/eNgEBYWZUY6WgOvrDVQ]|[server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Date: Fri, 20 Apr 2007 11:22:19 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2+/-puma.unideb.hu] Have a look at Mol2mol http://web.interware.hu/frenzy/mol2mol/ Tamas ----- Original Message ----- > From: "Martin Mueller martin.mueller|*|ime.fraunhofer.de" To: "Gunda, Tamas " Sent: Thursday, April 19, 2007 17:24 PM Subject: CCL: mol converters > > Sent to CCL by: Martin Mueller [martin.mueller[a]ime.fraunhofer.de] > > Hi, > > I'm looking for convertes for chemical structures. > (mol to smiles, mol to xyz etc.) > > I found: > > ChemAxons molconverter > http://www.chemaxon.com/product/molcon.html > which is free for academic use only > > Open Babel > http://openbabel.sourceforge.net/wiki/Main_Page > which seems to be "free" (GPL) > > ACD/Chemsketch > http://www.acdlabs.com/download/chemsk.html > > Any other available? > > Martinhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Fri Apr 20 07:06:01 2007 From: "Mathy Froeyen matheus.froeyen%%rega.kuleuven.ac.be" To: CCL Subject: CCL: is there any hydrophobic group comparable with Bromine atom Message-Id: <-34085-070420055936-32408-/r9cjpIQUS9LJ2SyxJK2GQ!^!server.ccl.net> X-Original-From: Mathy Froeyen Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 20 Apr 2007 11:01:14 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Mathy Froeyen [matheus.froeyen-.-rega.kuleuven.ac.be] There are some atom-based (including halogens) hydrophobicity / logp scales. See for instance SC Wildman, GM Crippen J Chem Inf Comput Sci 1999, 39, 868-873. Prediction of Physicochemical Parameters by Atomic Contributions. the best, mathy froeyen --------------------------- On Thu, 19 Apr 2007, Thomas Joseph alabarae . yahoo.com wrote: > > Sent to CCL by: "Thomas Joseph" [alabarae]-[yahoo.com] > is there any hydrophobic group comparable with Bromine atom. > Is there any website, which gives you the details and order of hydrophilic and hydrophobic atoms/groups > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Fri Apr 20 08:41:00 2007 From: "Andrew R Turner andrew.turner-#-ed.ac.uk" To: CCL Subject: CCL: Going from a Topology File to a .top File for an AMBER Forcefield Message-Id: <-34086-070420043603-7692-Mg8pfjGiQCzjNpv+Rkdt/g(-)server.ccl.net> X-Original-From: Andrew R Turner Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 20 Apr 2007 08:57:15 +0100 MIME-Version: 1.0 Sent to CCL by: Andrew R Turner [andrew.turner,+,ed.ac.uk] Jed, Have you tried using LEaP from the AMBER package itself? I have used it for both biomolecules and small organic fragments before and it was pretty simple. It will read in pdb files, check the topology and write it out in AMBER prmtop format. It is described in the AMBER manual. http://amber.scripps.edu/doc9/index.html There is a tutorial on creating new fragments for the AMBER forcefield (including charges, bond types etc.) at: http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm Regards Andy Quoting "Jed Zaretzki zaretj .. rpi.edu" : > > Sent to CCL by: "Jed Zaretzki" [zaretj++rpi.edu] > Hi all, > > I am looking for a tool which will go from a bare bones .pdb file to a .top > file. .pdb file should be considered a topology file. .top file can be > considered a detailed topology file with additional force field information > required to calculate partial charges upon the individual atoms of the > molecule (those partial charges are also in the file). I need this tool to > work for small molecules with at most 60 or 70 heavy atoms. I also need it > to work with an AMBER forcefield. > > > Initial Information in .pdb (or equivalent) file: > > Atom Type - no special types, equivalent to the atomic weight. > XYZ atomic coordinates > Bond Connectivity information, inluding whether they are single, > double or triple bonds. > > Final Information in .top (or equivalent) file. > > Atom Type - Specifically AMBER type with unique sigma and epsilon values. > XYZ atomic coordinates. > Bond Connectivity, including strength, defined by Leonard Jones > Potential of AMBER atom types. > Atom Partial Charges according to Amber Forcefield. > All valid angles. > All valid dihedral angles (torsions). > > Thanks a lot, > > Jed> > > > > ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner:_:ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Fri Apr 20 09:14:00 2007 From: "Van Dam, HJJ \(Huub\) h.j.j.vandam%dl.ac.uk" To: CCL Subject: CCL: Plastic candy bar wrappers Message-Id: <-34087-070420050833-25480-bJZEeHvWsU8tt9iyTYOO7g]*[server.ccl.net> X-Original-From: "Van Dam, HJJ \(Huub\)" Content-Class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Apr 2007 09:24:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam[A]dl.ac.uk] Hi Robert, The packaging machine probably has two welding bars to seal the packet (one seals the top end of a bar while the other one seals the bottom of the next bar). A knife goes between them to cut each candy bar loose. If the welding bars do not have the same temperature the effects you describe can easily happen as the polymer on the high temperature end can change more during the available welding time, alternatively the timing for the different welding bars might be slightly out. Just my guess. Huub ======================================================= Huub van Dam (h.j.j.vandam=-=stfc.ac.uk, +44-1925-603933) ======================================================= -----Original Message----- > From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net] Sent: 19 April 2007 18:59 To: Vandam, Huub Subject: CCL: Plastic candy bar wrappers Sent to CCL by: "Robert W. Zoellner" [rwz7001-*-humboldt.edu] Greetings All! So, I was fortifying myself for the remainder of the morning with a cup of tea and a candy bar (nothing but the best in nutrition!) and came upon this observation: When I attempted to tear open the candy bar wrapper from one end at the point where the two sides of the wrapper were sealed together by holding on to the overlapped sides and tearing, I could not get the plastic to begin to tear. However, when I did the same thing at the other end of the candy bar wrapper, the plastic tore easily. Does anyone with some knowledge of polymers know why I could tear the plastic from one end and not from the other? (There were little regular jagged edges at each end -- as if the plastic were cut with a pinking shears as would be done with cloth.) This is obviously not of great import, but I was hoping that someone would have an answer. All the best, Bob Z. Robert W. Zoellner, Ph.D. Professor and Chair Department of Chemistry Humboldt State University One Harpst Street Arcata, California 95521-8299 telephone: (707) 826-3244 fax: (707) 826-3279http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Apr 20 09:49:01 2007 From: "Caroline Norris cn29.:.sussex.ac.uk" To: CCL Subject: CCL: Relativistic and non-relativistic ECPs Message-Id: <-34088-070420053927-30414-rsXCkBOPUxEanamp/pezqA() server.ccl.net> X-Original-From: "Caroline Norris" Date: Fri, 20 Apr 2007 05:39:14 -0400 Sent to CCL by: "Caroline Norris" [cn29*|*sussex.ac.uk] Dear CCL, I was wondering if it's vaild to use a mixture of relativistic and non-relativistic ECPs within the same calculation? Currently I'm studying netural vanadium oxide and would like to use a relativistic ECP on the metal, but a non-relativistic ECP on the oxygen. Is this valid? Or will it cause complications within the calculation? Any comments would be greatly appreciated, Caroline Norris From owner-chemistry@ccl.net Fri Apr 20 10:24:01 2007 From: "Yousef Sharifi ysharifi : gmail.com" To: CCL Subject: CCL: Reactivity of zinc atom and hydrogen sulfide in the gas phase Message-Id: <-34089-070420093856-19346-VYyAPpYh18JHVmoLl/4ALA{:}server.ccl.net> X-Original-From: "Yousef Sharifi" Date: Fri, 20 Apr 2007 09:38:52 -0400 Sent to CCL by: "Yousef Sharifi" [ysharifi]_[gmail.com] Consider the reaction between zinc vapor and hydrogen sulfide in the gas phase. I used B3LYP/6-311+g(d,P) to find the reaction pathways for the reaction. Based on what I found!, If the zinc atom approaches sulfur atom first the reaction goes through a pathway with one transition state structure(46kcal barrier). But if the zinc atom approaches either of hydrogen atoms the reaction proceed through a different pathway with two intermediate complexes and two transition states(41kcal, and 49.6kcal). Is there anyway to determine the preferred pathway? Thanks Yousef, From owner-chemistry@ccl.net Fri Apr 20 11:15:01 2007 From: "Mehmed Zahid Ertem mzertem^gmail.com" To: CCL Subject: CCL:G: IEFPCM Solvent Optimization Convergence Message-Id: <-34090-070420110531-14838-CYNj6Fja6if2tjV+htBsIA-*-server.ccl.net> X-Original-From: "Mehmed Zahid Ertem" Date: Fri, 20 Apr 2007 11:05:27 -0400 Sent to CCL by: "Mehmed Zahid Ertem" [mzertem|,|gmail.com] Dear CCL'ers I am trying to optimize a transition state geometry of my system (that contains explicit water molecules) using IEFPCM method in G03. I came across with many error messages (genelogic tree error, Inv2 etc.). Recently, I am using [rmin=0.5 ofac=0.8 radii=bondi] keywords and optimizations seem to be going smooth. However, the transition state geometries (I have tried so far, an example is at the end) are not optimized with only one "NO" in maximum displacament. I have tried combinations of "gdiis, calcfc, calcall, different rmin ofac values including default ones, maxstep=1, cpcm method" but either the TS structure go to the products/reactants (like in different rmin ofac values) or again didn't converge with only one "NO" in maximum displacement. I will appreciate any help, thank you in advance, Mehmed Zahid Ertem Bogazici University Istanbul/Turkey B3LYP/6-31+G** opt=(maxstep=1,ts,noeigen,calcall) scrf=(iefpcm,solvent=water,read) .......... NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.004147 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.004277 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.004989 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.006690 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.005074 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.004804 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 Maximum Displacement 0.006398 0.001800 NO Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 NROrb= 381 NOA= 79 NOB= 79 NVA= 302 NVB= 302 .... .. . From owner-chemistry@ccl.net Fri Apr 20 15:22:01 2007 From: "Shobe, David David.Shobe]~[sud-chemie.com" To: CCL Subject: CCL: Reactivity of zinc atom and hydrogen sulfide in the gas phase Message-Id: <-34091-070420151452-8329-ewP6+t5sa4wd4z+6VdIvMg||server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Apr 2007 21:14:27 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe#sud-chemie.com] Yousef, In classical transition state theory, the path with the lowest maximum is the preferred reaction path. In your case the comparison is 46 < 49.6 (the 41 is irrelevant since it's not the maximum for that path), so the path with Zn approaching S is preferred. In real life there may be statistical-mechanics (e.g. trajectories approaching the HS..H...Zn transition state may be more probable) and/or quantum effects (e.g. tunneling of hydrogen atoms) which may change the answer. Especially since the two paths are so close in energy. --David -----Original Message----- > From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net] Sent: Friday, April 20, 2007 9:39 AM To: Shobe, David Subject: CCL: Reactivity of zinc atom and hydrogen sulfide in the gas phase Sent to CCL by: "Yousef Sharifi" [ysharifi]_[gmail.com] Consider the reaction between zinc vapor and hydrogen sulfide in the gas phase. I used B3LYP/6-311+g(d,P) to find the reaction pathways for the reaction. Based on what I found!, If the zinc atom approaches sulfur atom first the reaction goes through a pathway with one transition state structure(46kcal barrier). But if the zinc atom approaches either of hydrogen atoms the reaction proceed through a different pathway with two intermediate complexes and two transition states(41kcal, and 49.6kcal). Is there anyway to determine the preferred pathway? Thanks Yousef,http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Apr 20 17:58:01 2007 From: "Caleb Carlin calebcarlin]^[gmail.com" To: CCL Subject: CCL: Setting up a tip4p waterbox and running in Tinker Message-Id: <-34092-070420162354-2736-CxYxVehmUy5TIDVFajM8hQ ~ server.ccl.net> X-Original-From: "Caleb Carlin" Content-Type: multipart/alternative; boundary="----=_Part_110168_17504946.1177094624471" Date: Fri, 20 Apr 2007 14:43:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Caleb Carlin" [calebcarlin]*[gmail.com] ------=_Part_110168_17504946.1177094624471 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all, I am an undergraduate student trying to run a series of MD simulations using the various water molecules. I have a 50^3 Angstrom box with 500 water molecules based on the tip4p dimer that is included with Tinker. I have two questions that I have run into: Everytime I run a simulation, the program sets the ghost atom mass to 1.0 if it was 0.0 in the key file. Changing the mass to .0001 in the key file solves this problem, but is there a way to keep the mass at 0? Running the simulation with the "dynamic" program in Tinker results the program running on the processor but not calculating any of the steps. Below are the keywords in the key file. Is there something that is needed to run the tip4p model that is distinct from other models? parameters none archive printout 10 a-axis 50 group-molecule vdwtype LENNARD-JONES radiusrule GEOMETRIC radiustype SIGMA radiussize DIAMETER epsilonrule GEOMETRIC dielectric 1.0000 Thank you for any help, Caleb Carlin ------=_Part_110168_17504946.1177094624471 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all,
I am an undergraduate student trying to run a series of MD simulations using the various water molecules.  I have a 50^3 Angstrom box with 500 water molecules based on the tip4p dimer that is included with Tinker.  I have two questions that I have run into:

Everytime I run a simulation, the program sets the ghost atom mass to 1.0 if it was 0.0 in the key file.  Changing the mass to .0001 in the key file solves this problem, but is there a way to keep the mass at 0?

Running the simulation with the "dynamic" program in Tinker results the program running on the processor but not calculating any of the steps.  Below are the keywords in the key file.  Is there something that is needed to run the tip4p model that is distinct from other models?

parameters              none
archive
printout                10
a-axis                  50
group-molecule

vdwtype                 LENNARD-JONES
radiusrule              GEOMETRIC
radiustype              SIGMA
radiussize              DIAMETER
epsilonrule             GEOMETRIC
dielectric              1.0000

Thank you for any help,
Caleb Carlin
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