VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Feb 18 2012 - 16:39:55 CST

I will add that this is similar to what I did for an Fe ion coordinated by a
protein. Obviously you won't learn anything about binding/unbinding, but it
should at least represent the bound state reasonably well, vs. the
alternative of having the ion free (which may be interesting to look at for
comparison anyway). One additional note though: I had to create some new
atom types for coordinating residues in order to have unique parameters for
all the bonds/angles/dihedrals. Then I had to copy existing protein
parameters for those types to the new ones.

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Mayne, Christopher G
Sent: Saturday, February 18, 2012 3:40 PM
To: chiendarret_at_gmail.com
Cc: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Re: About FFTP with transition metal complexes

 

Francesco,

 

FFTK was designed primarily with small molecule organics in mind. I am not
familiar with the specifics of parameterizing metal complexes for CHARMM;
however, if it follows the same (or similar) workflow as organics, then FFTK
should, in principle, be applicable/useful.

 

To answer your questions directly:

 

1) FFTK relies heavily on QMtool for parsing Gaussian log files within the
charge optimization routine. Try loading the DFT calculation log file into
VMD using QMtool; if the optimization steps are properly loaded and you can
see step energies pushed to the TkConsole during the load, then it *should*
work in FFTK.

 

Note 1: you can still use FFTK to setup the calculation by changing the
Route details with in the "Gaussian Setting" section using the appropriate
Gaussian keywords

Note 2: make sure that you calculate separate single point energies for the
metal complex and a TIP3P water molecule at the same level of theory as used
in the water interaction calculation.

 

2) This is a more of a general psf/topology question and not directly an
FFTK question. Since I don't work with metalloproteins, I'm only guessing
here; hopefully someone else will chime in.

You should be able to leave all topologies in tact and write a patch to
adjust the partial charges for the ligating residues in addition to adding
bonds/angles/dihedrals necessary to describe the ligated complex.

 

 

Chris

 

 

Date: Sat, 18 Feb 2012 07:23:01 +0100
From: Francesco Pietra <chiendarret_at_gmail.com>
Subject: vmd-l: About FFTP with transition metal complexes

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