From owner-chemistry@ccl.net Sat Dec 30 00:15:01 2006 From: "Praveen Depa praveen_depa%yahoo.com" To: CCL Subject: CCL: protein simulation using AMBER Message-Id: <-33305-061222194909-17897-RsUCIPoDAgb6kyAJv6+kWw . server.ccl.net> X-Original-From: Praveen Depa Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: Praveen Depa [praveen_depa(~)yahoo.com] Dear CCLers, I am trying to simulate a protein with 36 residues (596 atoms) and explicit water using AMBER package. With a general input file shown below, total energy of the system (protein + water) and its components (electrostatic, bond, dihedral etc) are printed in the output file. Is there a way to output only the energy of the protein by just changing the input file? Does any one know if I need to change the source code to do it? Any suggestions in this regard are welcome. &cntrl imin = 0, irest = 1, ntxo = 0, ntx = 6, ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0, cut = 10, ntr = 0, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 100000, dt = 0.002, ntpr = 5000, ntwx = 5000, ntwr = 10000 / Thanx in advance -Praveen PhD Student Penn State Univ __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Dec 30 03:33:00 2006 From: "Itna Kcolc a_n_t_i_c_l_o_c_k|,|yahoo.com" To: CCL Subject: CCL: Code for Dead End Elimination (DEE) method Message-Id: <-33306-061222103720-17831-sWg8F8a/77EqIElgG4L4Xw^^server.ccl.net> X-Original-From: "Itna Kcolc" Sent to CCL by: "Itna Kcolc" [a_n_t_i_c_l_o_c_k||yahoo.com] Hello CCLers, Do u know about any freely available code available for the DEAD END ELIMINATION (DEE) method for protein energy optimization? Thanks in advance From owner-chemistry@ccl.net Sat Dec 30 13:18:00 2006 From: "Ross Walker ross(~)rosswalker.co.uk" To: CCL Subject: CCL: protein simulation using AMBER Message-Id: <-33307-061230025125-25730-wFg8JQggROeJHogp6+mtQA-x-server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 29 Dec 2006 22:51:09 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross .. rosswalker.co.uk] Dear Praveen, > With a general input file shown below, total energy of > the system (protein + water) and its components > (electrostatic, bond, dihedral etc) are printed in the > output file. Is there a way to output only the energy > of the protein by just changing the input file? Does > any one know if I need to change the source code to do > it? Any suggestions in this regard are welcome. No you would need to change the source code to do this. However, to do it directly (and correctly) would be pretty hard. The problem is that when you are using periodic boundaries with PME the electrostatic contribution is divided up into real space and reciprocal space parts. For any given atom some of the protein and solvent will be in the real space interaction part while some will be in the reciprocal space. Thus extracting out just the electrostatic energy due to protein-protein interactions would be difficult. Note, with rigid triangulated water energy terms corresponding to angles, dihedrals, 1-4 NB and 1-4 EEL come only from the protein. While the BOND, EEL and VDW terms contain contributions from both the protein and the solvent. Your best option for what you want to do, as far as I can tell, would be to post process your mdcrd file. You could strip the solvent from your mdcrd file and convert it to a series of amber restart files containing just the snapshots of the protein. Then create yourself a prmtop corresponding to just the protein. Create an input file with imin=1 and maxcyc=1. Then script it to run through each of your protein only restart files. The step 0 in the amber output from each run will then be the protein only energy. Note this would take some tweaking I think to get the protein image energy included as well but if the solvent box is large this may only be a small contribution and the gas phase protein energies may be good enough. Ps. it is best to post Amber related questions to the amber mailing list. See http://amber.scripps.edu for more info. All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross/a\rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Sat Dec 30 14:45:01 2006 From: "Reynier Suardiaz reynier.suardiaz%gmail.com" To: CCL Subject: CCL: basis sets updates Message-Id: <-33308-061222095912-12147-4s151BQXxUrvrjgJG9iAzw~!~server.ccl.net> X-Original-From: "Reynier Suardiaz" Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz++gmail.com] I would like to know about recent updates for the following basis sets: TZVP, EPR-II, EPR-III, aug-cc-pVTZ-J. best reynier From owner-chemistry@ccl.net Sat Dec 30 15:56:01 2006 From: "Gustavo Seabra gustavo.seabra~~gmail.com" To: CCL Subject: CCL: Statistical relevance of an average property Message-Id: <-33309-061221154612-32609-CoDX24wEm6RT32d5Bs+cvw[a]server.ccl.net> X-Original-From: "Gustavo Seabra" Sent to CCL by: "Gustavo Seabra" [gustavo.seabra{:}gmail.com] Hi Nicolas, Different properties converge differently from a MD trajectory. Basically, what you can do is to measure that property with different trajectory lengths and (hopefully) you'll see that, as the trajectory length increases, the property value should converge to one single number. I don't know exactly what you mean by 'ratio', but instead of just running a long MD you can try some method for enhanced sampling, like replica exchange for example, that can give you better sampling of the configurational space in less computational time. HTH, Gustavo. On 12/21/06, Nicolas Ferré nicolas.ferre:_:univ-provence.fr wrote: > Dear CCL, > > I am wondering what is the minimal ratio of structures extracted from a > MD trajectory that allows to compute an average property with > statistical relevance ? Does it depend on the length of the trajectory ? > If the ratio I want to use is not enough, shall I weight the property > according to a Boltzmann distribution ? > > Best regards, > > -- > NF From owner-chemistry@ccl.net Sat Dec 30 16:50:01 2006 From: "Axel Mathieu AMathieu[*]tranzyme.com" To: CCL Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Message-Id: <-33310-061221131811-29412-3BJK3toJGOsUzCaMkOZIEQ^server.ccl.net> X-Original-From: "Axel Mathieu" Content-Type: text/plain; charset="iso-8859-1" MIME-Version: 1.0 Sent to CCL by: "Axel Mathieu" [AMathieu#tranzyme.com] Hello Ralf, Did you ever hear of Molecular Conceptor (I http://www.molecular-conceptor.com/home.html)? Basically, it is a windows multimedia software package designed for teaching molecular modeling. Hope this helps, Axel -----Original Message----- > From: owner-chemistry-#-ccl.net [mailto:owner-chemistry-#-ccl.net] Sent: 21 décembre, 2006 09:55 To: Axel Mathieu Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Sent to CCL by: Ralf Tonner [Tonner-x-chemie.uni-marburg.de] Dear CCLers, since a few years the "Chemikum" exists at the University of Marburg (www.chemikum-marburg.de) as a possibility for pupils, adults and kids to learn to know the experimental world of chemistry and do some instructive experiments on their own. As a further extension to this project, our group has been asked to contribute with an "experiment" or interesting presentation from the computational chemistry side. As all of you know, presenting our topics even to chemists can be a tedious task, so I was searching the web for nice didactic "experiments" on the computer but unsuccessful up to know. Is anyone aware of a resource where to fetch some ideas or publicly available presentations/experiments which fulfill the requirements of being finished in at most half an hour without any pre-knowledge in quantum chemistry and at best let non-chemists gain some insight ? I would hardly have the time and educational knowledge of setting up something completely from scratch... so I am very grateful for any suggestions. Thanks for your help Ralf. -- Ralf Tonner Philipps Universität Marburg Fachbereich Chemie AK Frenking Hans-Meerwein-Straße 35032 Marburg Germany Tel.: +49-6421/28-27030 Tonner~!~chemie.uni-marburg.de From owner-chemistry@ccl.net Sat Dec 30 20:24:00 2006 From: "Andreas Klamt klamt]|[cosmologic.de" To: CCL Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Message-Id: <-33311-061221124942-9427-w7cKBpxAa3daA/RbQ5k0ow,,server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt,cosmologic.de] Dear Ralf, maybe you want ot use our COSMOtherm-Demo or COSMOtherm-Edu version. Users can select some compounds, see their surface polarities, and ask and answer questions as - do these 2 fluids mix? - why do they like/dislike eachother? - what is the vapor pressure of a compound? - what is the solubility in water, ethanol and/or a water/ethanol mixture - ... Answers are produced within a few seconds. I am not sure whether this is what you are looking for, but I can hardly think of something better suited for non-experts. You can download the demo version from http://www.cosmologic.de/downloads/CosmothermX_Demo_C21_0106_Windows.exe or for LINUX http://www.cosmologic.de/downloads/CosmothermX_Demo_C21_0106_Linux.tar.gz For the edu version please contact me. Regards Andreas Ralf Tonner Tonner.:-:.chemie.uni-marburg.de schrieb: > Sent to CCL by: Ralf Tonner [Tonner-x-chemie.uni-marburg.de] > Dear CCLers, > > since a few years the "Chemikum" exists at the University of > Marburg (www.chemikum-marburg.de) as a possibility for > pupils, adults and kids to learn to know the experimental > world of chemistry and do some instructive experiments on > their own. > > As a further extension to this project, our group has been > asked to contribute with an "experiment" or interesting > presentation from the computational chemistry side. > > As all of you know, presenting our topics even to chemists > can be a tedious task, so I was searching the web for nice > didactic "experiments" on the computer but unsuccessful up > to know. > > Is anyone aware of a resource where to fetch some ideas or > publicly available presentations/experiments which fulfill > the requirements of being finished in at most half an hour > without any pre-knowledge in quantum chemistry and at best > let non-chemists gain some insight ? > > I would hardly have the time and educational knowledge of > setting up something completely from scratch... > so I am very grateful for any suggestions. > > Thanks for your help > > Ralf. > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt:-:cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Sat Dec 30 21:52:00 2006 From: "Ralf Tonner Tonner]![chemie.uni-marburg.de" To: CCL Subject: CCL: "Experiments" in Quantum Chemistry for Non-chemists? Message-Id: <-33312-061221091621-7091-rxO0HRIoetH7oG76rW7+hg~!~server.ccl.net> X-Original-From: Ralf Tonner Content-Disposition: inline Content-Type: text/plain; charset="iso-8859-1" MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [Tonner||chemie.uni-marburg.de] Dear CCLers, since a few years the "Chemikum" exists at the University of Marburg (www.chemikum-marburg.de) as a possibility for pupils, adults and kids to learn to know the experimental world of chemistry and do some instructive experiments on their own. As a further extension to this project, our group has been asked to contribute with an "experiment" or interesting presentation from the computational chemistry side. As all of you know, presenting our topics even to chemists can be a tedious task, so I was searching the web for nice didactic "experiments" on the computer but unsuccessful up to know. Is anyone aware of a resource where to fetch some ideas or publicly available presentations/experiments which fulfill the requirements of being finished in at most half an hour without any pre-knowledge in quantum chemistry and at best let non-chemists gain some insight ? I would hardly have the time and educational knowledge of setting up something completely from scratch... so I am very grateful for any suggestions. Thanks for your help Ralf. -- Ralf Tonner Philipps Universität Marburg Fachbereich Chemie AK Frenking Hans-Meerwein-Straße 35032 Marburg Germany Tel.: +49-6421/28-27030 Tonner ~~ chemie.uni-marburg.de From owner-chemistry@ccl.net Sat Dec 30 23:34:01 2006 From: "Ajeet Singh ganguly- -csmcri.org" To: CCL Subject: CCL: TITAN SOFTWARE PROBLEM Message-Id: <-33313-061221060520-25844-A0j8IPdtf77aatQwlCZ01w/a\server.ccl.net> X-Original-From: "Ajeet Singh" Sent to CCL by: "Ajeet Singh" [ganguly=-=csmcri.org] Dear Sir/Madam, this mail is addressed to those using TITAN software for electronic structure calculations. We were using this program on Windows'98 and it was running fine. We upgraded our machine to Windows XP professional and Titan does not work with an error message that: "can't find the hardware key:exiting" There is a hardware key that should be plugged to the printer port to activate the porgram. Which is there is any case. We therefore, installed Windows'98 on one of the drives of that machine so that we can start Titan using Windows'98. Unfortunately, that also did not work with same error message. We have tried all HSAP drivers available in Aladdin web site: to update the hardware key function---nothing worked. TITAN was a joint venture of Schrodinger Inc. and Wavefuntion Inc. Now, I came to know that they have discontinued the service for TITAN for unknown reasons. If any CCL user have experienced this kind of problem and if there is any solution to this problem, , then it would be useful for us. with regards...Ajeet E-mail: ganguly/a\csmcri.org