Angel Herraez wrote: >Hello Ewen > > > >>I use Chime MEP surfaces for teaching basic ideas about molecular >>polarity, but it's not a lightly-taken decision. >> >>I've converted my old Chime resources into Jmol ones now, except the >>ones using MEP surfaces (and the dreaded Sculpt mode). Wanting to >>push on with my Chime --> Jmol conversions, I have a newbie question for >>Bob: What software would you use to calculate the MEP surface properly >>from a mol (or other) file? >> >> > >We've been recently trying to do this same thing. We found some solution in >freeware >Accelrys DS Visualizer, which can open the file (mol, pdb, whatever), >calculate and show >the MEP surface and export into MOL2 format, which keeps the calculated >charges. >However, sometimes the MEP coloring is not done by DSVis (don't know if it has >to do >with the original file or the program version). Also, it seems you need the >latest 1.7 >version to be able to export to MOL2 (1.5 won't offer this format). >After that, Jmol will open the MOL2 and display the MEP either from the pop-up >menu or >from the equivalent isosurface command, something like > isosurface molecular map mep > > I am still exploring other possibilities. For macromolecules, there is the > pdb2pqr + APBS >route --still I'm not getting successful results--. > > > >>PS Sorry if I missed it Bob, but did anything happen with lipophilic >>potential colouring of surfaces? >> >> > >I think this is even more misterious than MEP; as far as I know, nobody says >how it's >calculated and, certainly, Jmol cannot do it now.. > > Once again (even I really understang Jmol philosophy) I speak for MEP calculation feature (if possible). MEP is useful for educational purposes: structure-property relationships, solubility, ... I know that I can calculate MEP and include the data in suitable file format. But in low level education, it is common using ACD/Chemsketch and similar program (not able to calculate MEP) with exporting to MOL (a most common format at this field). I use Jmol filter for Moodle and database module for creating and downloading structures by students, which are not able to perform MEP calculations. Therefore students cannot see nor MEP nor partial charges as was in Chime.
From my point of view, I dare to think about "MEP approximation" and "MLP approximation" feature in addition to using MEP data directly from file. For possible MEP (and lipophilic potential) calculation I discover: Chemistry Development Kit; Package org.openscience.cdk.charges http://cdk.sourceforge.net/api/org/openscience/cdk/charges/package-summary.html Some links to Chime calculation is present below: *ag name: **set mep|mlp function* *Description: *Specifies the function used to determine MEP or MLP distance when rendering a surface. This command is often used in conjunction with "set mep|mlp distance" to establish a distance "cutoff". *Syntax: *set mep function {1 or Gaillard|2 or Audry|3 or Fauchere|4 or Hartshorn|5 or Coulomb} or set mlp function {1 or Gaillard|2 or Audry|3 or Fauchere|4 or Hartshorn} Some of the calculations used: *Function* *Description* Gaillard or 1 *MLP = Sum(f * e^(-d/2))1-natoms* f = Lipophilic value for atom i d = distance from point to atom (angstroms) Gaillard, P., Carrupt, P.A., Testa, B. and Boudon, A., J.Comput.Aided Mol.Des. 8, 83-96 (1994) Audry or 2 *MLP = Sum(f/(1 + d))1-natoms* f = Lipophilic value for atom i d = distance from point to atom (angstroms) Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. A new approach to structure-activity relations: the "molecular lipophilicity potential". Eur. J. Med. Chem. 1986, 21, 71-72. Fauchere or 3 *MLP = Sum(f * e^(-d))1-natoms* f = Lipophilic value for atom i d = distance from point to atom (angstroms) Fauchere, J. L.; Quarendon, P.; Kaetterer, L. Estimating and representing hydrophobicity potential. J. Mol. Graphics 1988, 6, 203-206. Hartshorn or 4 Mike Hartshorn's weighted distance algorithm Coulomb or 5 Coulomb's law distance function (same as rasmol potential distance function) Many thanks for language switching, Bob, you work quicker than I write e-mails ;-) -- S pozdravem / Yours sincerely Martin Slavik __________________________________ Martin Slavik Department of Chemistry Faculty of Education Technical university of Liberec Halkova 6, 461 17 Liberec Czech Republic ____________________________________ ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
