I am trying to determe several electrostatic properties of several ion channels under various circumstances. I am wondering if anybody has suggestions or answers to the following:
1) When APBS determines ion and solvent accessibility, will it recognize the pore domain as accessible and implicitly fill it with solvent (assuming its radius is larger than solvent molecules/atoms)? For instance, in http://www.research.ibm.com/journal/rd/453/baker.html is the microtubule ultimately 'filled' with the "solvent of dielectric 78.54 and ionic strength of 150 mM"?
2) Supposing that one wanted to allow water molecules of the solvent into the channel pore, but exclude ions. Is this possible in APBS? What strategies are available to accomplish this (are there parameters in the input file which can be specified to exclude ions from the pore, such as kappa, but not water; would it be better to modify the input PQR and fill the pore with water ahead of time; should I make my own kappa map?)?
3) I am also interested in determining the change in the system's electrostatic energy when an ion is placed at various points in the channel pore and all other mobile ions are excluded from this region (possibly water excluded as well). Is it feasible to add a second molecule to the system that consists of a single ion located at the desired position, or would it be better, or not make a difference if instead I modified the PQR/PDB of the original molecule by adding a HETATM for the ion at the desired position?
4) If the electrostatic energy calculation of question 3) is performed in a vacuum (ion concentration = 0 and solvent dielectric = 1, solvent radius = 0... is that correct?), is the electrostatic energy essentially the energy required to assemble the molecule by bringing its constituents from infinity?
Any insights, answers or help would be much appreciated.
Department of Biomedical Engineering
Montreal, Quebec, Canada
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