Hi Davide,

You can try the PARSE forcefield instead in this case.

Good luck,


On Wed, Sep 9, 2009 at 5:43 PM, Davide Mercadante <dmer018@aucklanduni.ac.nz> wrote:
Dear APBS users,

I have run a job on the pdb2pqr server specifying the protonation state of the residues in my protein (at pH3) but using AMBER force field.
The server computed my question but it says that all the residues were reset to a protonation state of 7 because AMBER force field doesn't support that protonation state.

I need to run three jobs in which the protonation states are 3, 6 and 7.5. Please, can you advice me which are the best force fields to use in these pH ranges?

Thanks in advance for the help.


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Yong Huang, D.Sc.

Center for Computational Biology
Washington University School of Medicine