Last revision: 10-11-2014

The pKmod values of the C-terminus were re-calculated and corrected. 


Last revision: 18-01-2012 

*The model compounds presented in this directory contain the atomic
charges of GROMOS 54A7 force field and pKmod values calculated for
this force field analogously to what was done in ref[1].

*This directory contains .st files *only* for the sites that were
parametrized using CpHMD simulations. If you want to use other titrable
sites (e.g., ARG) or non-titrable sites (e.g., SER, THR; as done in rigid
calculations), you should build your own st-XXX directory with those extra
files (e.g., copied from a directory without "_Fit").

*The files corresponding to the different proton isomers (tautomers)
contain "tau" in their designation (e.g. TYRtau1.st and TYRtau2.st).
Bear in mind that the pKmod of each tautomer is different from the
global pKmod (check ref[1] for more details).

*If you do not wish to include tautomers in your calculations, use the
files containing "all" in their name (e.g. TYRall.st). These files
choose the proton isomer that appears in the force field and present
the global pKmod of the site.

*The files with the prefix CTALA, corresponding to the C-terminus of
alanine, can be easily transformed in any other type of C-terminus by
simply substituting all occurrences of "ALA" (in the name of the files
and inside the files) by any other residue name. 

E.g. The C-terminus site of leucine can be created like this: 
sed 's/ALA/LEU/g' CTALAall.st > CTLEUall.st

Actually, something like this is done by the getst program included in
the meadTools package. The same applies to the N-terminus sites that
can be created from the files with prefix NTALA. Proline is a special
case, having its own files (prefix NTPRO).
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ref[1]: Machuqueiro, M, Baptista, AM (2011) "Is the prediction of pKa
values by constant-pH molecular dynamics being hindered by inherited
problems?" Proteins, 79, 3437.
