hello everybody this is my first question since I use chimera, more than 3 years ago, and I would like to know if is it possible to add atom type in the MMTK basis set ? I actually work on a molecule containing platinium, and I can't run mopac because there is no description. I'm looking for some description files , and I found this : /antechamber/dat/antechamber/*****.DAT which is the good one and which is the way to modify it ? thank's for your answer and excuse me for my english..... best regards -- ================================================= NAUTON Lionel Ingénieur d'études. Laboratoire de Synthèse Et Etude de Systèmes à Intérêt Biologique UMR6504 : université Blaise Pascal – CNRS 24, avenue des Landais – Campus des Cézeaux 63177 AUBIERE Cedex France Tel : 04 73 40 55 06 mèl : lionel.nauton@univ-bpclermont.fr <mailto:lionel.nauton@univ-bpclermont.fr> site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm <http://seesib.univ-bpclermont.fr/site_web/pageaccueil.html> =================================================
Hello Lionel, Are you trying to run "addcharge" or "minimize"? If "addcharge" to calculate partial charges on some Pt complex (e.g. cisplatin or carboplatin): Nonstandard residues are sent to Antechamber, but that program is only meant to be used on organic molecules (C,H,O,N,S,P,F,Cl,Br,I), not metal complexes or inorganic species. See the antechamber site: http://amber.scripps.edu/antechamber/tips.html I think you have to use some other program that can handle metal complexes to derive partial charges. I don't think it is possible to simply edit some antechamber data files to get it to work on such compounds. If "minimize" and you just wanted to treat the Pt as a monatomic ion with integer charge: I had thought it possible to add a metal ion type by editing a parameter file. However, I have not been successful at minimizing a structure with the "new" type even when the file appears to include the necessary parameters. Maybe there is an additional step that I don't know about. So currently my best answer is that it is not possible, but if we find a way, we will send another message. (I may be wrong given my lack of success, but I think the relevant parameter file within the Chimera installation is lib/python2.5/site-packages/ MMTK/ForceFields/amber/amber_parm99 ) Sorry about that, Elaine ----- 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 On May 30, 2008, at 5:52 AM, Lionel Nauton wrote:
hello everybody this is my first question since I use chimera, more than 3 years ago, and I would like to know if is it possible to add atom type in the MMTK basis set ? I actually work on a molecule containing platinium, and I can't run mopac because there is no description. I'm looking for some description files , and I found this : /antechamber/dat/antechamber/*****.DAT which is the good one and which is the way to modify it ? thank's for your answer and excuse me for my english..... best regards
participants (2)
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Elaine Meng -
Lionel Nauton