Thread: [Apbs-users] APBS apolar solvation calculation
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From: Neha G. <n.g...@gm...> - 2009-03-27 03:21:56
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Dear List, I have seen in apolar calculation that the value of gamma varies from 0.105 to 210 kJ mol-1 Å-1. Also, according to the alkane tutorial, press= 0.2394, bconc= 0.033428. If I keep this 2 terms as 0, the volume term gets cancelled and I end up with only SASA. In Amber, this apolar calculation is gamma*SASA+ cavity offset. There is no volume term. Is there any correlation with the equations in AMBER and in APBS? My system has a protein complex to anionic carbohydrate and I am performing PBSA calculations for such a system.What are the recommended values for such system for apolar solvation calculation? Help is much appreciated. Regards, Neha Gandhi |
From: Nathan B. <ba...@bi...> - 2009-03-28 01:48:36
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Hello -- I have seen in apolar calculation that the value of gamma varies from 0.105 > to 210 kJ mol-1 Å-1. Also, according to the alkane tutorial, press= > 0.2394, bconc= 0.033428. If I keep this 2 terms as 0, the volume term gets > cancelled and I end up with only SASA. Yes, that is correct. > In Amber, this apolar calculation is gamma*SASA+ cavity offset. There is no > volume term. Is there any correlation with the equations in AMBER and in > APBS? The APBS equations are an expanded version of this simpler model as described in Wagoner and Baker. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proceedings of the National Academy of Sciences of the United States of America (2006) vol. 103 (22) pp. 8331-6. > My system has a protein complex to anionic carbohydrate and I am performing > PBSA calculations for such a system.What are the recommended values for such > system for apolar solvation calculation? Unfortunately, carbohydrates have not been parameterized for this more complex model -- and I'm actually not aware of surface tension values for the simpler model (although they could certainly exist). Sorry, Nathan > > Help is much appreciated. > Regards, > Neha Gandhi > > > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |