Thread: RE: [Apbs-users] How to calculate the protein-membrane electrostatic interactions?
Biomolecular electrostatics software
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From: Nathan B. <ba...@bi...> - 2004-10-25 13:24:49
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Hello -- A number of folks have done calculations with PBE solvers and membranes; Benoit Roux has several papers describing these approaches. This has been done with APBS but requires some work on your part. In particular, you'll need to setup the dielectric profile of the membrane as an OpenDX-format map which is read into APBS. Please see the APBS user manual and OpenDX manipulation tools/examples for more information on how to do this. Good luck! -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker > -----Original Message----- > From: apb...@ch... > [mailto:apb...@ch...] On Behalf Of Ting Guo > Sent: Monday, October 18, 2004 10:18 AM > To: apb...@ch... > Subject: [Apbs-users] How to calculate the protein-membrane > electrostatic interactions? > > Hello, > > In my current project, I hope to computationally analyze the > electrostatic interaction between a protein and an > immediately juxtaposing lipid bilayer. Is there any easy way > to do this calculation with APBS, or is there anything > example that I can use as reference, since I'm not very > familiar with statistical mechanics? > > Thank you in advance! > > Sincerely, > Ting Guo > > > > > -------------------------------------------------------------- > ----------------------- > AOC(冠捷)六大随心技,开启"随心视"代 http://design.163.com/aocmonitor/index. html > 网易126专业电子邮局,为您提供卓越电子邮件服务,http://www.126.com/ > 全国最大的免费邮箱,260兆空间12兆附件,强力杀毒反垃圾,界面无广告 > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > |
From: Ting G. <fe...@16...> - 2004-11-05 13:54:34
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Thank you very much! And how to deal with water molecules in the model? For example, if both of the protein and membrane models (in PQR) contain some water molecules, do I have to eliminate whem manually before starting the calculations? As in APBS calculation I have already assumed the electrostatic properties of the medium, will these water molecules intervene with obtaining good results? Thanks in advance, Ting Guo |
From: Nathan B. <ba...@bi...> - 2004-11-05 14:08:01
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Yes and no -- it depends what the water molecules are doing... You might look at some papers we wrote on this: Lin J-H, Baker NA, McCammon JA. 2002. Bridging the implicit and explicit solvent approaches for membrane electrostatics. Biophysical Journal 83(3):1374-1379. Wagoner J, Baker NA. 2004. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. Journal of Computational Chemistry 25(13):1623-9. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker > -----Original Message----- > From: apb...@ch... > [mailto:apb...@ch...] On Behalf Of Ting Guo > Sent: Friday, November 05, 2004 5:54 AM > To: apb...@ch... > Subject: [Apbs-users] Re: How to calculate the > protein-membrane electrostatic interactions? > > Thank you very much! And how to deal with water molecules in > the model? For example, if both of the protein and membrane > models (in PQR) contain some water molecules, do I have to > eliminate whem manually before starting the calculations? As > in APBS calculation I have already assumed the electrostatic > properties of the medium, will these water molecules > intervene with obtaining good results? > > Thanks in advance, > Ting Guo > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > |
From: Frank D. D. <fr...@wa...> - 2004-10-26 22:11:51
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Hey All, I am getting the following error message at the beginning of my output files for simple solvation calculations: asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. The calculation seems to go ahead and complete ok, although some values have had significant error. Does anyone recognize this error message? -- Frank Ducheneaux Caltech Division of Chemistry m/c 127-72 Pasadena, CA 91125 (626)395-2689 |