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From: Nathan Baker <baker@bi...> - 2009-06-18 22:40:11
|
Hello -- > I am trying to create the input file to cmpute the electrostatic > potential of a protein. The APBS calculation will be useful to run a > Brownian Dynamics to understand the features of a complex between > the protein and a polysaccharide. > > I have been reading carefully how to create an input file but I am > not an expert and I find difficult to find the right flags to insert > in it. > Please can you give me guidelines to "which parameters to include in > the file" and "how to chose the right flags for those parameters". PDB2PQR (http://pdb2pqr.sf.net/) will generate input files for you that can be modified/customized for your particular application. This should provide a starting point that you can expand upon using the APBS documentation. > As well, which parameters and flags to insert in the .in file are > the best for a saccharide? I'm not aware of any particular parameters for this but hopefully someone on the APBS mailing list might have a suggestion. Good luck, Nathan > Thanks in advance for your precious help. I will appreciate is so > much. > > All the Best, > Davide -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis Web: http://bakergroup.wustl.edu/ |