Last revision: 17-11-2015 

*The model compounds presented in this directory contain the atomic
charges of GROMOS 54A7 force field and the pKmod values in water
calculated for this force field according to ref[1] and ref[2].

*The files correspond to different proton isomers (tautomers)
containing "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[2] for more details).

*The termini files for the different amino acid residues are
automatically created by CpHMD from the files with the prefix CTALA
(C-terminus) and NTALA (N-terminus). For instance, 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 in the
meadTools package that is used inside CpHMD. The same applies to the
N-terminus sites that can be created from the files with prefix
NTALA. This means that CpHMD can adapt these files to correctly treat
the termini and you don't need to worry about it. Proline is a special
case, having its own files (prefix NTPRO).
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ref[1]: Carvalheda, CA, Campos, SRR, Machuqueiro, M, Baptista, AM
(2013) "Structural Effects of pH and Deacylation on Surfactant Protein
C in an Organic Solvent Mixture: A Constant-pH MD Study" J Chem Inf
Model, 53, 2979, Erratum in J Chem Inf Model (2015) 55, 206.

ref[2]: Machuqueiro, M, Baptista, AM (2011) "Is the prediction of pKa
values by constant-pH molecular dynamics being hindered by inherited
problems?" Proteins, 79, 3427.
