[Apbs-users] Re: convert uhbd input to apbs
Biomolecular electrostatics software
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From: Nathan A. B. <ba...@ch...> - 2003-12-19 14:14:21
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Hi Fabrice -- I get this question fairly frequently so I'm going to Cc my reply to the APBS mailing list. There are two ways to get the Coulombic energy of a complex: 1. Use Coulomb's law (apbs/tools/manip/coulomb) and scale by the appropriate dielectric coefficient. 2. Solve Poission's equation with a homogeneous dielectric coefficient to determine the energies of protein A, protein B, and the A-B complex. The proteins' atoms must stay at exactly the same place on the grid for each calculation; likewise, the grid spacing, position, etc. cannot change between calculations. The Coulombic energy change for forming the complex is then: E(AB) - E(A) - E(B) Of the two ways, #1 is almost always preferable. Fabrice Leclerc <Fab...@ma...> (12-19-2003 00:14:50+0100): >Hi Nathan, >I'm interested in the coulombic energy between 2 molecules. The >calculation using the "coulomb" utility is pretty straightforward. How >do you extactly extract this term from the numerical calculations ? >Thanks. >Fabrice. > > >On Friday, December 12, 2003, at 03:27 PM, Nathan Baker wrote: > > >>Hi Fabrice -- >> >>You always need to perform a reference calculation with APBS to >>remove the self-energies. In other words, if you perform a solvation >>energy calculation, then the uniform dielectric result is your >>"self-energy". The Coulombic energies can either be obtained from >>numerical (apbs) or analytical (tools/manip/coulomb) manipulations. >> >>Thanks, >> >>Nathan >> >>-- >>Nathan A. Baker, Assistant Professor >>Washington University in St. Louis >>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: Fabrice Leclerc [mailto:Fab...@ma...] >>Sent: Friday, December 12, 2003 6:42 AM >>To: ba...@bi... >>Subject: Re: convert uhbd input to apbs >> >>Hi Nathan, >>thanks for your quick reply. >>I'm wondering whether it's possible to decompose the total >>electrostatic energy into its different contributions rather than by >>per-atom components with the calcenergy flag. I mean to have the >>electrostatic coulombic and self energies as well. >> >>On Thursday, December 11, 2003, at 02:47 PM, Nathan Baker wrote: >> >>Hello -- >> >>While you cannot convert UHBD input to APBS in a straightforward way >>(there are internal routines...), you can convert APBS to UHBD with >>the utility in the apbs/tools directory. That should do what you >>need. >> >>For the parallel focusing calculations, you should choose your fine >>and coarse grid dimensions/spacings to match what you would normally >>give to UHBD. Based on the list you gave below, I'd suggest >> >>1. dime 65 65 65, glen 128 128 128 >>2. dime 97 97 97, glen 97 97 97 >>3. dime 97 97 161, glen 48 48 80 >> >>This will preserve the grid spacing (important for comparisons) but >>will result in slightly larger calculation domains. >> >>Thanks, >> >>Nathan >> >>-- >>Nathan A. Baker, Assistant Professor >>Washington University in St. Louis >>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: Fabrice Leclerc [mailto:Fab...@ma...] >>Sent: Wednesday, December 10, 2003 5:59 PM >>To: ba...@ch... >>Subject: convert uhbd input to apbs >> >>Hi Nathan, >>I'm doing some tests with APBS (0.2.6) and want to compare with some >>previous calculations I've done with UHBD. Is there any way to easily >>convert a UHBD input file into a APBS input file ? >>In the parallel version, it seems to be necessary to specify cglen >>and fglen but it not obvious to me what values I should use to >>reproduce a setting similar to what I had with UHBD. In the UHBD >>calculation, I use to have 3 calculations (2 focussing) with >>different grid sizes: >> >>1. spacing 2.0 dime 51 56 65 >>2. spacing 1.0 dime 61 70 88 >>3. spacing 0.5 dime 83 100 137 >> >>I have to say I couldn't figure out how to get a similar setting with >>APBS. Can you give me some hint ? Thanks. >>Fabrice. >> >> >>\ /\ >>\/ \______________________________________ >>/\ >>A--U Fabrice Leclerc, Ph.D. >>(----) Laboratoire de Maturation des ARN >>G--C et Enzymologie Moléculaire (MAEM) >>\/ UMR 7567 CNRS-UHP Nancy I >>/\ Faculté des Sciences, B.P. 239 >>U--A 54506 Vandoeuvre-lès-Nancy Cedex >>(----) Tel. (33) 3 83 68 43 17 >>C--G Fax. (33) 3 83 68 43 07 >>\/ Fab...@ma... >>/\ _____________________________________ >>/ \ / >>\/ >> >> > > End of message from Fabrice Leclerc. -- 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 PGP key: http://cholla.wustl.edu/~baker/pubkey.asc |