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
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
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Lionel Nauton