Re: [Apbs-users] Reproducing solvation free energies (PARSE) with APBS
Biomolecular electrostatics software
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From: Marc B. <ba...@sm...> - 2004-10-15 09:47:45
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HI Jessica, thanks a lot for your comment. My reading of the original PARSE paper is a bit different from yours. From the paragraph (directly extracted from the paper): [..]The boundary between solute and solvent is the "molecular surface" which is obtained from the van der Waals and reentrant surfaces, the latter being generated by rolling a solvent-sized probe over the van der Waals surface (probe radii of 0.0 and 1.4A for vacuum and water were used).[..] I concluded that srad should be 0.0 in the reference calculation. Am I going wrong ? (but in any case I also tried with 1.4 .. results get worse). I do use 0.0 nonpolar hydrogen radii, or even just don't include the nonpolar hydrogens. If you want to try some of the structures, I put pqr and input file at http://www.shaman.ibpc.fr/parse.tar (this might not be exactly the same input file as the one I initially attached, as I did some more trial and error runs. And maybe some pqr's are not yet ok, as I just attached all files I played with). Best wishes, Marc >> Hi Marc, >> >> I noticed that you used srad 1.4 in your solvated calculation and srad 0.0 >> in your reference calculation in the attached input file. This will >> certainly off set your results from the original PARSE results. Both >> should be 1.4, indicating a molecular surface traced by a 1.4 Angstrom >> solvent probe. >> >> If this was just a typo and/or you still get different results, I >> would be curious to see your input pqr files. Are you using 0.0 nonpolar >> hydrogen radii? >> >> Best regards, >> >> Jessica Swanson >> McCammon Group >> UCSD - Chem/Biochem -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:ba...@sm... - http://www.marc-baaden.de FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217 |