Frequently asked questions for PIPSA
(Protein Interaction Property Similarity Analysis

1.   I have pdb files of my proteins, but PIPSA fails to proceed them, what is wrong ?
2.   PIPSA did not superpose my proteins
3.   How do I change ionic strength value to 150 mM from default 50 mM ?
4.   I have more than 999 proteins and PIPSA does not work
5.   I have many proteins and similarity calculations take ages
6.   I want to change one protein pdb file, should I re-calculate all pairwise similarities now ?
7.  How do I run PIPSA on WindowsXP / MacOSX ?
8.  Why there are 2 versions mkapbsin.f and mkapbsin-apbs-ot-0.3.2.f ?
9.   I have electrostatic potentials as DELPHI grid files, can I compare them with PIPSA ?
10.  How do I compare one part of my protein with its another part ?
11.  Can I use PIPSA for non-protein molecules ?
12.  I can not get any correlation between the interaction fields and experimental kinetic parameters in qPIPSA analysis, what is wrong ?
13.  What are the two ways of running PIPSA ?

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