hi all,
Are there the topology and parameter files available for the cytochrome c
heme? The difference from the case of destributed files is that the heme
here has two covalent bonds with the protein (two cysteins). Also there
is a methionine ligand instead of CO.
I did patch the heme to the protein to establish these covalent bonds. After
this, molecular structure generation required some new bonds, angles and
dihedrals and their parameters to be defined. I did define those but I'm not
sure if the values I'm giving are correct. The reason of my suspicions is
that during the refinement the total and VDW energies remain higher than
one would expect. It results (I guess) in not quite appropriate Wa values
required and therefore the positional refinement does not converge well.
For example, the gradient remains quite high (around 7.) regardless on
the number of refinement cycles.
Please send me an e-mail directly if you don't have a ready answer but
would like to hear more details about the problem.
Thanks for any help,
R.Sanishvili
sanishvili at anbiw4.sbc.anl.gov
