From: Mike Osborne <michael.osborne@um...> - 2005-09-17 18:56:08
I am wondering if APBS can be used to look at changes in the
electrostatics at different pH's? If so does anyone have any helpful
hints or if not is there software (and visulaisation) that can?
Thanks very much in advance..
Iric-Institut de Recherche en Immunovirologie et Cancérologie
Université de Montréal
Montreal, Quebec, H3T 1J4
Ph: (514) 343 6111 ext. 0534(NMR)/ 0595(Office)/ 0610(Wet lab)
Fax: (514) 343 7379
Hi Mike -
Although APBS itself is not capable of directly generating electrostatic
potentials at different pHs, you can generate PQR files at different pHs
using PDB2PQR/PropKa and then input each PQR file into APBS for
PDB2PQR is available as a server at
or as a downloadable command-line tool from
Make sure you use PropKa to assign protonation states at each desired
pH, and then use the resulting PQR files as inputs to APBS.
From there I'm not sure if there is a good way quantitatively compare
much more than the high-level (total energy, etc) information from each
APBS run, but you may at least be able to graphically compare the results.
Please let me know if you have any further questions -
Mike Osborne wrote:
> Hello everyone
> I am wondering if APBS can be used to look at changes in the
> electrostatics at different pH's? If so does anyone have any helpful
> hints or if not is there software (and visulaisation) that can?
> Thanks very much in advance..
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