From owner-chemistry@ccl.net Thu Sep 13 08:07:00 2007 From: "Gonzalo Jim nez Os s gonzalo.jimenez**unirioja.es" To: CCL Subject: CCL:G: MM parameters in ONIOM calculations Message-Id: <-35144-070913080554-10801-ot6J4rFeXFC3oqHCHwQR0A##server.ccl.net> X-Original-From: "Gonzalo Jim nez Os s" Date: Thu, 13 Sep 2007 08:05:50 -0400 Sent to CCL by: "Gonzalo Jim nez Os s" [gonzalo.jimenez#%#unirioja.es] (I hope this e-mail address still works...) Dear CCL'ers, I have observed some striking inconsistency when running ONIOM calculations and removing (or killing) some redundant internal coordinates. Whereas the high system model energy (the QM part) is identical in both types of calculations (with and without removing internal coordinates), as expected, the low system model and real energies (the MM part) are somewhat different. I do believe that the energy of a given system (and consequently its optimization process) should not be affected by the removal of some internal coordinates, unless MM parameters are generated depending on the self-defined internal coordinates matrix. So, my question is: is there any way to tell Gaussian not to generate a full set of MM parameters as a function of the self-defined internal coordinates matrix? or, in other words, is the user able not to include some terms in MM energy for some selected atoms (for example, to include all terms by default but to include only non-bonded terms between atoms A and B)? Thank you very much in advance. Regards, Gonzalo Jimnez-Oss From owner-chemistry@ccl.net Thu Sep 13 08:41:00 2007 From: "Gonzalo Jim nez-Os s gjimenez .. unizar.es" To: CCL Subject: CCL:G: MM parameters in ONIOM calculations Message-Id: <-35145-070913080156-10052-0TPh7aCun2NxYKmI5//6Yg===server.ccl.net> X-Original-From: "Gonzalo Jim nez-Os s" Date: Thu, 13 Sep 2007 08:01:52 -0400 Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez|-|unizar.es] Dear CCL'ers, I have observed some striking inconsistency when running ONIOM calculations and removing (or killing) some redundant internal coordinates. Whereas the high system model energy (the QM part) is identical in both types of calculations (with and without removing internal coordinates), as expected, the low system model and real energies (the MM part) are somewhat different. I do believe that the energy of a given system (and consequently its optimization process) should not be affected by the removal of some internal coordinates, unless MM parameters are generated depending on the self-defined internal coordinates matrix. So, my question is: is there any way to tell Gaussian not to generate a full set of MM parameters as a function of the self-defined internal coordinates matrix? or, in other words, is the user able not to include some terms in MM energy for some selected atoms (for example, to include all terms by default but to include only non-bonded terms between atoms A and B)? Thank you very much in advance. Regards, Gonzalo Jimnez-Oss From owner-chemistry@ccl.net Thu Sep 13 12:42:00 2007 From: "Juan C. Drosos jdrosos * gmail.com" To: CCL Subject: CCL: Semiempirical Electron Affinities 2 Message-Id: <-35146-070912130631-28875-AM0UO36eQGtpRkR9CD3Aog a server.ccl.net> X-Original-From: "Juan C. Drosos" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 12 Sep 2007 12:03:43 -0400 MIME-Version: 1.0 Sent to CCL by: "Juan C. Drosos" [jdrosos]|[gmail.com] I partially agree with professor Hutchinson or Hutchison, semiempirical methods are not very reliable for calculating electron affinities if you are looking for analytic values. if you just want to compare trends on the values for this property on compound series PM3 is OK. a deeper analysis, including fukui values, superdelocalizabilities partial charges and so on may require an electron correlation method. I evaluated redox properties (on organic compounds) for my PhD thesis comparing semiempirical results with DFT (B3LYP-6-311G**, 3-21G**) the trends for EA were comparable. but as i told you a deeper anlalysis requires a stronger method like DFT. excuses for my bad english, and i hope this information help. On 9/12/07, Gustavo L.C. Moura gustavo a mercury.chem.pitt.edu wrote: > > Sent to CCL by: "Gustavo L.C. Moura" [gustavo##mercury.chem.pitt.edu] > Dear CCL readers, > Last week I asked to the list: > > > I have been asking myself how I can obtain reliable values for the > > electron affinities of organic molecules employing semiempirical methods > > like AM1, PM3 or RM1. What I mean is that these semiempirical methods > > were parameterized to yield good values for the ionization potentials (it > > is part of their parameterization process). But, what about electron > > affinity? Should I also use Koopmans like in the case of ionization > > potentials? What are your opinions? > > I have received only one answer from Geoff Hutchison that said: > > > My experience is that AM1 and PM3 have very poor electron affinity > > calculations. As you say, it's not in their parameterization, so they > > are very unreliable. I only tend to believe EA from higher level > > calculations like B3LYP or better. > > Supposedly, the new PM6 method, part of MOPAC 2007 has electron > > affinities included in the parameterization. > > I would like to thank Prof. Hutchison for his answer and > I will keep looking for ways of calculating reliable electron affinities > using MOPAC. > Sincerely yours, > Gustavo L.C. Moura> > > > From owner-chemistry@ccl.net Thu Sep 13 13:17:00 2007 From: "Gemma Kinsella maynooth],[bell.maths.tcd.ie" To: CCL Subject: CCL: Protein-Protein scoring - non standard residue. Message-Id: <-35147-070913130403-5036-K8TqRzRDkxFz0ZdCcmUZDw,+,server.ccl.net> X-Original-From: "Gemma Kinsella" Date: Thu, 13 Sep 2007 13:03:59 -0400 Sent to CCL by: "Gemma Kinsella" [maynooth,+,bell.maths.tcd.ie] Hi all, I have a number of protein-protein complexes that I wish to be able to rank/score. However, one of the proteins has a number of CGU residues (GAMMA-CARBOXY-GLUTAMIC ACID) which need to be considered. Would anyone know of a protein-protein scoring function/docking software that is able to handle non-standard residues or is amenable to the addition of new residue topologies/details? I have the parameters, charges etc. needed. Most that I have come across so far just ignore the CGU residues. Any help pointing me in the right direction would be much appreciated. Gemma Kinsella gkinsell++tcd.ie School of Biochemistry and Immunology Trinity College Dublin Ireland From owner-chemistry@ccl.net Thu Sep 13 14:08:00 2007 From: "Prashanth Athri athriprashanth::yahoo.com" To: CCL Subject: CCL: Using TIP5P water model in AMBER MD simulations Message-Id: <-35148-070913113945-7355-AM0UO36eQGtpRkR9CD3Aog- -server.ccl.net> X-Original-From: "Prashanth Athri" Date: Thu, 13 Sep 2007 11:39:40 -0400 Sent to CCL by: "Prashanth Athri" [athriprashanth+/-yahoo.com] Dear CCL'ers, I am using AMBER with TIP5P water model to simulate a DNA + ligand + Solvent system. To begin with this might not be an AMBER related issue, it might be something to do with th nature of TIP5P water model. So please see if you can comment on the problem even if you are using other MD simulation software. Thanks in advance. I am having the following question regarding TIP5P usage. I am comparing results of TIP5P and TIP3P water (trying) wrt DNA+ ligand simulation. (recent publications suggest TIP5P is being unnecessarily ignored) In xleap, (part of Amber), when I use the following commands: 1. solvateoct co TIP3PBOX 8.0 2. solvateoct co TP5 8.0 Both models add different number of residues (1) Gives the following results: Scaling up box by a factor of 1.255439 to meet diagonal cut criterion Solute vdw bounding box: 26.332 28.427 46.640 Total bounding box for atom centers: 66.727 66.727 66.727 (box expansion for 'iso' is 97.7%) Solvent unit box: 18.774 18.774 18.774 Volume: 155327.486 A^3 (oct) Total mass 81340.042 amu, Density 0.870 g/cc Added 4066 residues. (2) Gives the following: Solvent has no box, so preparing by making box including vdw (Use 'setBox centers' first if box was pre-equilibrated) Scaling up box by a factor of 1.255439 to meet diagonal cut criterion Solute vdw bounding box: 26.332 28.427 46.640 Total bounding box for atom centers: 66.727 66.727 66.727 (box expansion for 'iso' is 97.7%) Solvent unit box: 3.708 3.678 3.502 Volume: 155327.486 A^3 (oct) Total mass 54099.850 amu, Density 0.578 g/cc Added 2554 residues. My question is why is there such a huge difference in the number of water molecules added and the density? 4066 TIP3P waters are added whereas only 2554 TIP5P are added. Thanks in advance Best wishes, Prashanth From owner-chemistry@ccl.net Thu Sep 13 15:16:01 2007 From: "Guenter Grethe ggrethe|*|comcast.net" To: CCL Subject: CCL: 2008 Herman Skolnik Award recipient Message-Id: <-35149-070913143505-6723-hn6Mm5GcMEgzcs3TqPSQBQ . server.ccl.net> X-Original-From: "Guenter Grethe" Date: Thu, 13 Sep 2007 14:35:02 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe . comcast.net] 2008 Herman Skolnik Award Winner Announced The Division of Chemical Information of the American Chemical Society is pleased to announce the recipient of the 2008 Herman Skolnik Award. Professor Gerald M. Maggiora has been a leader in chemical information and a force of innovation for many years. As a cheminformatics pioneer, solid contributor, practitioner, strong advocate, mentor, teacher, advisor, consultant and a true student of the scientific method, Gerry has worn several hats in both academia and in the industry. His outstanding contributions have had a tremendous impact within and outside the cheminformatics community. Prof. Maggiora has a remarkable breadth of knowledge and unparalleled ability to take ideas originating from seemingly unrelated disciplines, synthesize them, and apply them successfully to important problems in chemical information science. He is the author of nearly 150 scientific papers, and the editor of the book Concepts and Applications of Molecular Similarity published in 1990 by John Wiley & Sons, which has become one of the true classics in the field. Prof. Maggiora has made several contributions to the field of chemical information that include: the development of chemical & biological information systems; molecular similarity and diversity analysis; applications of fuzzy set theory; applications of neural networks; applications of computer-assisted decision making algorithms; applications of information theory; assessment of consistency in medicinal chemists review; chemistry space analysis and comparing compound collections; directed screening methods; focused screening methods; structure-activity relationships and activity cliffs; and applications of rough-set theory. Gerry received a B.S. in chemistry (1964) and a Ph.D. in biophysics (1968) from the University of California at Davis. He did postdoctoral work in theoretical chemistry at the University of Kansas and spent 15 years there as a faculty member in the Departments of Chemistry and Biochemistry. In 1985 he joined what was then The Upjohn Company as the Director of Computational Chemistry, a position he held until 1998. From 1998 to 2003 he served as a Senior Research Advisor and Fellow at the Pharmacia Corporation. In 2003, he joined the faculty of the University of Arizona, Tucson, College of Pharmacy and the BIO5 Institute as a Professor of Pharmaceutical Sciences. He serves on several scientific advisory, editorial and grant review boards. Guenter Grethe CINF Awards Chair ggrethe-#-comcast.net From owner-chemistry@ccl.net Thu Sep 13 16:57:00 2007 From: "Bill Ross ross*cgl.ucsf.edu" To: CCL Subject: CCL: Using TIP5P water model in AMBER MD simulations Message-Id: <-35150-070913163808-31429-Rr4o5aWi4ZjsqLT0dVNTgw]![server.ccl.net> X-Original-From: Bill Ross Date: Thu, 13 Sep 2007 13:05:59 -0700 (PDT) Sent to CCL by: Bill Ross [ross__cgl.ucsf.edu] > 4066 TIP3P waters are added whereas only 2554 TIP5P are added. Per the answer on the amber list, with TIP3P a pre-equilibrated box is used to solvate, while w/ TIP5 a single molecule is replicated on a grid to solvate, with less optimized packing. Instructions for TIP5P tell how to use TIP3P box to solvate, then convert to TIP5P. Bill Ross