Thread: [Apbs-users] Fwd: Potential calculation using APBS
Biomolecular electrostatics software
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From: Nathan B. <ba...@cc...> - 2007-10-24 16:07:13
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Hello -- Todd forwarded your e-mail message to me. I'm not completely sure of the specifics of what you're trying to do. However, I think the apbs/tools/mesh/multivalue.c will, with a bit of modification, probably accomplish what you need to do. Thanks, Nathan ---------- Forwarded message ---------- From: Todd Dolinsky <to...@cc...> Date: Oct 18, 2007 8:13 AM Subject: Fwd: Potential calculation using APBS To: Nathan Baker <ba...@cc...> This email went just to me; it'd probably be better for the mailing list... Todd ---------- Forwarded message ---------- From: ch...@ri... <ch...@ri...> Date: Oct 17, 2007 5:19 PM Subject: Potential calculation using APBS To: to...@cc... Hi, Todd I am using APBS to calculate the electrostatic potential of a solavated protein. Do you have a program (or even a few lines of C code) that can be used to read the pot.dx and then store these valule in a 1d array like POT[nx*ny*nz]. I would like to use this potential for further calculations. I am using C for coding. Thanks! Mary Hongying Cheng -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Kin S. S. L. <si...@ch...> - 2007-10-24 17:54:17
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Hello everyone. I have the problem to run the APBS in pymol and it always give me the error regarding to some atoms is unassigned and please remove those atom before you run APBS again. Is there any solution for that? Thank you very much Sing |
From: Nathan B. <ba...@cc...> - 2007-10-24 18:04:16
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Hello -- I'd recommend using PDB2PQR to generate your PQR file -- either through PyMOL I'd the web server. That may fix this problem. Good luck, Nathan -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ On Oct 24, 2007, at 12:54, Kin Sing Stephen Lee <si...@ch...> wrote: > Hello everyone. > > I have the problem to run the APBS in pymol and it always give me > the error regarding to some atoms is unassigned and please remove > those atom before you run APBS again. > > Is there any solution for that? > > Thank you very much > > Sing > > |