VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Feb 18 2012 - 00:23:01 CST

My aim is to parameterize a transition metal complex for a
metalloproteins. Two questions about FFTP, a most waited tool which
going to foster a lot of research work.

(1) Calculation of partial charges. When a transition metal is
involved, a single-point HF would be inappropriate. Current literature
about any type of dealing with such complexes suggests to go on - from
beginning to end - with DFT, with higher basis set for the metal or
metal ion. Who has specific experience for CHARMM ff to this regard.
In any case, is FFTP prepared to accept the results (partial charges,
geom data, force constants) from a DFT type of calculation? If so I
could try to apply the plugin to my case.

(2) As there is no tutorial yet for FFTP, it is not yet clear to me
how to bind the parameterized metal complex to its protein. I make an
example: for a metal ion bound to HIS and ASP residues, I make a model
including a portion only of the HIS and ASP residues, while carrying
out partial charge and bond data (geometry and force constants) for
that model. Correspondingly, I have a protein from which the portion
included into the metal complex has been removed. What about the
procedure to establish chemical bonds between the abridged protein and
the metal complex? (i.e., the equivalent of the command "bond xxx
yyy" with Amber's LEaP).

Thanks
francesco pietra