Has anyone noticed major differences between the results obtained in
GRASP when using the method...
1) Read| PDB file
2) Read|Radius Charge File(+Assign)
3) Build|Molecular Surface|All atoms
4) Calculate|New Potentail Map
5) Calculate|Pot. via Map at Surfaces/Atoms|All atoms|All surfaces
...and those generated with the same pdb in Pymol/APBS-tools?
The results I see from this differs from Pymol/APBS-tools as follows...
1) The pqr generated by pymol or the web pdb2pqr web site has -15
net charge whereas GRASP's amber.crg only creates a -11 net charge.
2) The GRASP display shows small patches of positive charge on a
e-lvl scale (say -6 to +4) whereas the Pymol/APBS-tool electrostatic
surface only shows negative (red) surfaces on this same scale).
I have to move the middle position of the e-lvl scale in Pymol to
the negative side (off zero) and lower the positive limit on the e-lvl
meter to actually see any patches of positive charge in pymol.
What is the likely cause of this difference in potential maps between
the coarse GRASP electrostatic display and Pymol/APBS-tools' output?
Even with the additional negative charges I hadn't expected the small
areas of positive charge shown in GRASP to be reduced quite so much.
Thanks in advance for any advice.
ps This is using Pymol 0.97 or 0.98beta33 and APBS 3.2.2.