From owner-chemistry@ccl.net Mon Mar 20 08:44:00 2006 From: "Irena Efremenko irena.efremenko_+_weizmann.ac.il" To: CCL Subject: CCL:G: modredundant with molecular mechanics Message-Id: <-31242-060320084222-12089-Dnz12I81SPgCT0Ucq1T6JQ^^server.ccl.net> X-Original-From: Irena Efremenko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 20 Mar 2006 15:02:25 +0200 MIME-Version: 1.0 Sent to CCL by: Irena Efremenko [irena.efremenko/./weizmann.ac.il] Dear CCLers, Does somebody here know how to force Gaussian03 to read modredundant section in molecular mechanics optimization. I want to perform relaxed PES scan for large (~600 atoms) system in redundant coordinates. Thanks in advance, Irena Efremenko -- ****** Dr. Irena Efremenko Dept. of Organic Chemistry Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972 8 9343680 FAX: +972 8 9344142 Email: irena.efremenko|,|weizmann.ac.il ****** From owner-chemistry@ccl.net Mon Mar 20 14:33:00 2006 From: "Rafael R. Pappalardo rafapa#,#us.es" To: CCL Subject: CCL: TTM2-F implementation Message-Id: <-31243-060320142716-23281-mRUrwddZPKD1zs/G7shebA%a%server.ccl.net> X-Original-From: "Rafael R. Pappalardo" Date: Mon, 20 Mar 2006 14:27:14 -0500 Sent to CCL by: "Rafael R. Pappalardo" [rafapa,+,us.es] Does anybody knows if there is any publicly available programs which implements the TTM2-F water force field? Thanks in advance. Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. of Seville (Spain) From owner-chemistry@ccl.net Mon Mar 20 15:30:00 2006 From: "Marcin Krol mykrol[-]cyf-kr.edu.pl" To: CCL Subject: CCL: Scaling frequency in PCM Message-Id: <-31244-060320132640-15350-070kFbdsCnN5V6NYnQ5SvQ ~ server.ccl.net> X-Original-From: Marcin Krol Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 20 Mar 2006 18:30:12 +0100 (MET) MIME-Version: 1.0 Sent to CCL by: Marcin Krol [mykrol||cyf-kr.edu.pl] Dear All, I am running frequency calculations in CPCM/HF/6-31+G(d) and I wonder what the scaling factor could be. I probably cannot use 0.9163 advised for vacuum HF/6-31+G(d) calculations. Is it then better not to use the sacling factor at all? What I want from freq calculations is ZPE to get free energies of different tautomers of the same molecule in water. Since I am interested in relative stabilities of tautomers and scaling factor is probably not so important (ZPEs will be pretty the same anyway). Or am I wrong? Thank you in advance for your suggestions Best regards marcin From owner-chemistry@ccl.net Mon Mar 20 16:12:04 2006 From: "Nicolas Ferre nicolas.ferre*univ-provence.fr" To: CCL Subject: CCL: How to select residues Message-Id: <-31245-060320095008-11263-fNepvFDDrYlCO3lYNImSxg%a%server.ccl.net> X-Original-From: "Nicolas Ferre" Date: Mon, 20 Mar 2006 09:50:06 -0500 Sent to CCL by: "Nicolas Ferre" [nicolas.ferre]^[univ-provence.fr] Dear CCL'ers, I'd like to select and save a small part of a pdb file. Actually I want to select all the residues inside a given sphere centered on an amino-acid. I know I can use RasMol's "select within (expression)" but it results in selecting some atoms, not whole amino-acids. Obviously I can look at the selection using "show selected" and copy/paste every amino-acid label, but this is a rather tedious task. Alternatively I can use Molden, but as far as I known, it only shows the corresponding amino-acids without giving the possibility to save them in a file. If I am wrong, please correct me. If not, do you know any free software allowing such residue selection and saving ? Best regards, Nicolas From owner-chemistry@ccl.net Mon Mar 20 16:47:01 2006 From: "John Kendrick john,+,kendrick.me.uk" To: CCL Subject: CCL: Cutting Edge Approaches to Drug Development at University of Bradford Message-Id: <-31246-060320082431-9118-O1flqmxHVVNezk+9F0fIZw() server.ccl.net> X-Original-From: "John Kendrick" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 Mar 2006 12:23:03 -0000 MIME-Version: 1.0 Sent to CCL by: "John Kendrick" [john]=[kendrick.me.uk] The second Cutting Edge Approaches to Drug Development meeting will take place at the University of Bradford on April 24th and 25th 2006. The meeting is organsed jointly by the Molecular Modelling Group of the Royal Society of Chemistry and the Institute of Pharmaceutical Innovation at the University of Bradford The aim of this meeting is to critically review the current status of computational chemistry as applied to pharmaceutical development and formulation and to highlight and discuss emerging technologies that could make a future impact in this field. The meeting covers issues from molecular properties through materials properties to assembled dosage forms and is structured into 3 sessions; > From molecules to crystals Polymorphism and crystal properties Formulation and processing Speakers include Professors Peter York, Martyn Guest, Mark Rodger, Sally Price, Marcus Neumann, Liz Colbourn, Susan Craw and David Gethin. More details about event and details for registration are available from the web site. http://www.ipi.ac.uk/resources/events/event/cutting-edge-approaches-to-drug- development-ii Dr John Kendrick Institute of Pharmaceutical Innovation University of Bradford Bradford BD7 1DP Tel: +44(0)1274 236101 Fax: +44(0)1274 236166 Email: J.Kendrick(~)bradford.ac.uk From owner-chemistry@ccl.net Mon Mar 20 17:21:01 2006 From: "Warren DeLano warren**delsci.com" To: CCL Subject: CCL: How to select residues Message-Id: <-31247-060320171204-22283-snU6ELEK669uhUAxnSVTrg(-)server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 Mar 2006 14:15:05 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren/a\delsci.com] Nicholas, > If I am wrong, please correct me. If not, do you know any > free software allowing such residue selection and saving ? PyMOL has a rich atom selection language for such tasks: load protA.pdb select my_sele, byres (protA within 10 of resi 54) save subset.pdb, my_sele etc. http://delsci.com/rel/099 As "free", PyMOL is entirely free if you compile it from the open-source code, and our convenient precompiled binaries are free to evaluate, free for full-time students, and free when used on prexisting public data. Payment for other uses is via the honor system. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren#delsci.com > -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] > Sent: Monday, March 20, 2006 1:45 PM > To: Warren DeLano > Subject: CCL: How to select residues > > Sent to CCL by: "Nicolas Ferre" [nicolas.ferre]^[univ-provence.fr] > Dear CCL'ers, > > I'd like to select and save a small part of a pdb file. > Actually I want to select all the residues inside a given > sphere centered on an amino-acid. > I know I can use RasMol's "select within (expression)" but it > results in selecting some atoms, not whole amino-acids. > Obviously I can look at the selection using "show selected" > and copy/paste every amino-acid label, but this is a rather > tedious task. > Alternatively I can use Molden, but as far as I known, it > only shows the corresponding amino-acids without giving the > possibility to save them in a file. > If I am wrong, please correct me. If not, do you know any > free software allowing such residue selection and saving ? > > Best regards, > > Nicolas > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the # sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From owner-chemistry@ccl.net Mon Mar 20 17:59:00 2006 From: "Elaine Meng meng%cgl.ucsf.edu" To: CCL Subject: CCL: How to select residues Message-Id: <-31248-060320174209-6655-aSv8VTT+9wmDMeJ9yNnvww~~server.ccl.net> X-Original-From: Elaine Meng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 20 Mar 2006 14:02:03 -0800 Mime-Version: 1.0 (Apple Message framework v746.3) Sent to CCL by: Elaine Meng [meng^^^cgl.ucsf.edu] Hi Nicolas, In Chimera, you can write out the coordinates of whatever set of atoms is selected. One way to select atoms is by specifying a zone. For example, to select all atoms of residues with any atom within 4.5 angstroms of any atom in residue 12 of chain A: command> select :12.a zr<4.5 or to use an atom-based cutoff instead of residue-based: command> select :12.a za<4.5 There are many possible variants, such as ":12.a^-^ca" to only use the CA atom, or ":fad" to specify a residue named FAD, or using Select menu instead of a command to make the selection. After making the selection, choose Actions... Write PDB. To get a list of the residues instead of the coordinates, use Actions... Write List. Chimera can be downloaded free for noncommercial use, see http://www.cgl.ucsf.edu/chimera/ I hope this helps, Elaine On Mar 20, 2006, at 1:18 PM, Nicolas Ferre nicolas.ferre*univ- provence.fr wrote: > Sent to CCL by: "Nicolas Ferre" [nicolas.ferre]^[univ-provence.fr] > Dear CCL'ers, > > I'd like to select and save a small part of a pdb file. Actually I > want to select all the residues inside a given sphere centered on > an amino-acid. > I know I can use RasMol's "select within (expression)" but it > results in selecting some atoms, not whole amino-acids. Obviously I > can look at the selection using "show selected" and copy/paste > every amino-acid label, but this is a rather tedious task. > Alternatively I can use Molden, but as far as I known, it only > shows the corresponding amino-acids without giving the possibility > to save them in a file. > If I am wrong, please correct me. If not, do you know any free > software allowing such residue selection and saving ? > > Best regards, > > Nicolas > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > ----- Elaine C. Meng, Ph.D. meng^-^cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Mon Mar 20 18:33:01 2006 From: "Andrew D. Fant fant=-=pobox.com" To: CCL Subject: CCL: Time for a Current Protocols in Computational Chemistry? Message-Id: <-31249-060320181122-29351-VB2Z8veLqFIsK3KE5MKGNQ*server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 20 Mar 2006 17:06:28 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant=pobox.com] Afternoon all, For the past couple of weeks, I have been kicking around an idea and I would like some feedback from the larger community. Those here who deal with wet biology and biochemistry or bioinformatics have probably come in contact with the Current Protocols series. For those who aren't familiar with it, Current Protocols is a set of loose-leaf reference volumes ( or their electronic equivalent) that provide a standard method for common lab operations and enough of the theory behind it. They have a volume for bioinformatics as well, with articles such as "Multiple Sequence Alignment using ClustalW and ClustalX". The website, for those who are interested is http://www.currentprotocols.com . My question/proposal is simple. Has the time come for the computational chemistry community to have a similar resource available? I don't necessarily think that this need be a volume in the aforementioned series, but someplace that someone needing to perform a calculation that they aren't familiar with can go to get a sense of what others would consider the "right" way to do it. So, what say ye? Would this be considered useful, and, more to the point, are there any practitioners out there who are interested in talking in more depth about what form and content this project could take on? Thanks, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant.*.pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Mon Mar 20 19:10:00 2006 From: "Roger Kevin Robinson r.robinson]*[imperial.ac.uk" To: CCL Subject: CCL:G: modredundant with molecular mechanics Message-Id: <-31250-060320115328-1400-8+4vcRJZBkwaSgsIpMiJ2Q##server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 20 Mar 2006 16:48:32 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson,imperial.ac.uk] Hi, Im trying to rotate the methyl group on CH2CCH3 using the scan option. My input file is listed below. I've associated the hydrogens on the methyl together and then tried to rotate it. However I dont think the group is completely rotated because the results I am getting do not show a high enough change in energy and because it just looks wrong when I load the .log file into gaussview. Can any one tell me what im doing wrong ? Thansk Roger %chk=/home2/rkr79/gaussian/C7H7OO/scans/t-C3H51.chk %mem=6MW %nproc=1 # scan ub3lyp/6-31g(d,p) geom=connectivity Title Card Required 0 2 C H 1 B1 H 1 B2 2 A1 C 1 B3 3 A2 2 D1 C 4 B4 1 A3 3 D2 H 5 B5 4 A4 1 D3 H 5 B6 4 A5 6 D4 H 5 B7 4 A6 6 D5 B1 1.07947785 B2 1.07429198 B3 1.32536491 B4 1.48887310 B5 1.08760730 B6 1.08476175 B7 1.08474310 A1 116.55338488 A2 121.66621285 A3 136.00396434 A4 110.81891406 A5 110.80676392 A6 110.80788943 D1 -179.97841932 D2 -179.94904922 D3 -0.70235405 s 23 15.0 D4 119.49414900 D5 -120.86797802 1 2 1.0 3 1.0 4 2.0 2 3 4 5 1.0 5 6 1.0 7 1.0 8 1.0 6 7 8 From owner-chemistry@ccl.net Mon Mar 20 20:16:00 2006 From: "Fiona Case fhcase#,#hotmail.com" To: CCL Subject: CCL: A review of force fields Message-Id: <-31251-060320113648-31143-mDuARxOM/hGAxZK2BlgRJg*_*server.ccl.net> X-Original-From: "Fiona Case" Content-Type: text/plain; format=flowed Date: Mon, 20 Mar 2006 11:36:24 -0500 Mime-Version: 1.0 Sent to CCL by: "Fiona Case" [fhcase###hotmail.com] Hello, I'd like to suggest that you have two questions to answer: Which forcefield to use, and which method to use (MD/MC, which flavor?). If you make a wise choice of forcefield, but a poor choice of method, you will still get poor results. Also, when you look at many of the "forcefield review" papers they consider intramolecular interactions (bond lengths, bond angles, vibrational frequencies obtained from isolated molecules, etc.). Unless you are trying to predict properties of molecules in a vacuum, intermolecular interations are at least as important. Most do not consider the effect of temperature or pressure, nor do they provide guidence on the transferability of the forcefields (what will happen if your molecule is slightly different to the one used in the published study?) This lack of validation/verification/guidence has been identified as a major limitation to the useful application of force field based methods. http://www.chemicalvision2020.org/pdfs/compchem.pdf http://fluidproperties.org/Vision-and-Strategic-Plan-5-Feb-06.pdf However, there is some good news: Some organizations are attempting to solve this problem. If you take a look at the publications and websites that have resulted from their efforts you will already see some guidence on forcefield and method selection for "useful" simulations. 1) The Industrial Fluid Properties Simulation Collective (of which I am a member)http://fluidproperties.org/ 2) The BioSimGrid, http://www.biosimgrid.org/ 3) The protein folding challenges: http://predictioncenter.org/ 4) If you are looking at something that is a crystal, see the Crystal Structure Prediction challenges: http://scripts.iucr.org/cgi-bin/paper?S0108768105016563 You could encourage every "modeling expert" you meet (particularly in academia) to support these efforts. The problems you are facing in trying to select a forcefield and method to use for your work are shared by everyone attempting to apply these methods. It is of benefit to us all that more validation/verification/guidence becomes available so that molecular simulations methods become "useful" to the wider world, and particularly in industry. Fiona Case ----Original Message Follows---- > From: "Carlos Nunez carlos_javierna*o*yahoo.com" Reply-To: "CCL Subscribers" To: "Case, Fiona " Subject: CCL: A review of force fields Date: Thu, 16 Mar 2006 20:57:41 -0500 Sent to CCL by: "Carlos Nunez" [carlos_javierna{:}yahoo.com] Hi, See this: MacKerell A. D. Jr. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25: 1584-1604. Hasta la proxima vez, Carlos N.http://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 Mon Mar 20 21:13:00 2006 From: "Robinson, James James.Robinson%%evotec.com" To: CCL Subject: CCL:G: modredundant with molecular mechanics Message-Id: <-31252-060320211204-32617-h65nYlogQQrtNsJG9qauQg##server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 21 Mar 2006 02:12:07 -0000 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson|evotec.com] Use #opt=(z-matrix) nosymm ; instead of scan keyword. James -----Original Message----- > From: owner-chemistry|*|ccl.net [mailto:owner-chemistry|*|ccl.net] Sent: 21 March 2006 00:35 To: Robinson, James Subject: CCL:G: modredundant with molecular mechanics Sent to CCL by: Roger Kevin Robinson [r.robinson,imperial.ac.uk] Hi, Im trying to rotate the methyl group on CH2CCH3 using the scan option. My input file is listed below. I've associated the hydrogens on the methyl together and then tried to rotate it. However I dont think the group is completely rotated because the results I am getting do not show a high enough change in energy and because it just looks wrong when I load the .log file into gaussview. Can any one tell me what im doing wrong ? Thansk Roger %chk=/home2/rkr79/gaussian/C7H7OO/scans/t-C3H51.chk %mem=6MW %nproc=1 # scan ub3lyp/6-31g(d,p) geom=connectivity Title Card Required 0 2 C H 1 B1 H 1 B2 2 A1 C 1 B3 3 A2 2 D1 C 4 B4 1 A3 3 D2 H 5 B5 4 A4 1 D3 H 5 B6 4 A5 6 D4 H 5 B7 4 A6 6 D5 B1 1.07947785 B2 1.07429198 B3 1.32536491 B4 1.48887310 B5 1.08760730 B6 1.08476175 B7 1.08474310 A1 116.55338488 A2 121.66621285 A3 136.00396434 A4 110.81891406 A5 110.80676392 A6 110.80788943 D1 -179.97841932 D2 -179.94904922 D3 -0.70235405 s 23 15.0 D4 119.49414900 D5 -120.86797802 1 2 1.0 3 1.0 4 2.0 2 3 4 5 1.0 5 6 1.0 7 1.0 8 1.0 6 7 8http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt