Eplicit solvent

[Roy Assis]

Hello 

I'm trying to run APBS for a pdb file of a protein with an explicit solvent. The file was created using GROMACS. 

I don't have alot of knowledge in the issue, I was wandering if 1) APBS can make such calculations and 2) How do I make a PQR from my PDB (that includes water), the pdb2pqr server does not support water to my understanding, and is ommiting them during the charge assignment. 

Finally, 3), does APBS with explicit solvent (generated during an MD run) is more reliable with APBS with implicit solvent (that include a-priori assumptions).

Thank you 

Roy 

[Nathan Baker]

Hi Roy --

Are you referring to a calculation with a full box of explicit water or just a few explicit waters bound to the protein?  I wouldn't recommend the former; there's no good reason to use implicit solvent in those conditions.  If you do need to evaluate electrostatics for the entire explicit solvent simulation box, VMD has some nice tools that will allow you do that.

For the latter case of a few explicit waters, PDB2PQR should be able to parameterize your file and assign charges and radii to the waters.

Good luck,

Nathan

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