From: mashaojie163 (mashao_jie_at_163.com)
Date: Wed Nov 14 2007 - 21:58:39 CST
Dear Sir:
How can I use amber force field to calculate protein.
I think that I should do this according to the following 3 steps.
1) I should generate a psf file and a coord file. Which top file should be used to gererate the psf file? Where can I download the topfile? What type is the coord file?? Is PDB OK??
2) I should have a amber parameter file. Which parameter file should I choose? Where can I download the parameter file??
3) I should modify the configure file acoording
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html.
then I run NAMD.
So, there are so many questions before I excute the 3rd step. Please help me and answer the questions in detail! Thank you very much??
Best Regards
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Shaojie Ma
Institute of Nano Science
Nanjing University of Aeronautics and Astronautics
mashaojie_at_nuaa.edu.cn
Nanjing 210016, China
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