Dear Francesco,
>> I would test and demonstrate that these CHARMM parameters work in
>> association with the Amber FF you wish to use.
> You are right, I am planning to run short NVE simulations to observe if
> energy drift occur.
> Do you have any better suggestion that can help me to test the method's
> effectiveness?
I do not know the structure you wish to study and the story you want
to report by MD. You could follow some key distances/dihedrals in the
iron complexes or in the vicinity of this iron complex.
> This is the most frequent problem, but before I used to submit job with
> method not belonging to DFT familiy.
Yes
> Now I submitted the job using GAUSSIAN with a DFT method.
> The input geometry I am using cames from the X-ray structure. I hope
> this is good enough.
You also need to extract some atoms representative of your
iron-complex from the PDB structure... Thus, you need to keep in mind
that you will have to insert this complex in your PDB file; this mean
the FF library you will generate has be compatible with existing FF
libs from the Amber distribution or at least compatible with another
FF lib you will generate in a second step...
When using R.E.D. Server this is generally achieved by using
intra-molecular charge constraint(s); see for instance:
http://q4md-forcefieldtools.org/RED/resp/
> Regarding this option, thank you for the willingness. I wanna wait for
> the response of the already implemented options.
ok
> What I think is that, as general suggestion, you should implement some
> option that skipping geometry optimization calculating
> electrostatic potential directly on the user-supplied structure.
I think you misunderstood what means "user defined options" in R.E.D.
Server ;-) this means new options in QM such as basis set and DFT
methods which are not yet implemented.
. q4md-forcefieldtools.org we are interesting in finding approaches
which leads to reproducible charge values, and by characterizing all
the steps required in charge derivation; this is well handled for
organic molecules. For bioinorganic molecules, this is another story.
This is not because you have an accurate set of x y z Cartesian
coordinates for a given complex that the QC code will generate a
correct wavefunction/wanted orbitales; there are many pitfalls here.
We are interesting in solving all these pitfalls by fully
characterizing the minimum generated by QM (obviously the resulting
cpu cost can be very important). We do NOT want to implement
approaches where a structure is not characterized by geometry
optimization.
It is easy to skip the geometry optimization step (see
http://q4md-forcefieldtools.org/RED/FAQ-II.php#2 for intance) and
input a non-defined set of Cartesian coordinates for MEP
computation/charge fitting for a metal complex. One can also derive
charges for the metal center by hand: we are not interested by such an
approach...
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 01 2011 - 07:30:03 PDT
