onetwo wrote:
Hello All,
I am new in this field, and I want to do simulation study on one of the
protein conatining a metal ion and study its ability to form
co-oridnation bond with other ligand, which is not defined in GROMOS
force field which I have tried. If this choice of force field is correct
for such type of study ?
I have read Gromacs Manual Chapter 5, also I am following this gromacs
mailing list for quite some time to get a help on how to include a new
metal ion or a new ligand in their simulation and they have been refered
to refer to the
http://www.gromacs.org/Documentation/How-tos/Parameterization,
but in this its not mentioned that how to actually do parameterization
neither in manual it has been told on how to generate it ( due
apologies,,I know, I may be wrong )
The manual will not cover every possible topic. Parameterization is described
in the primary literature for the force field you wish you use. "GROMOS" is not
very specific - there are numerous parameter sets within this class of force field.
and it is more difficult for a person like me who doesnt have much
knowledge in this field, so if someone can please help me guiding how to
do parameterisation, I know this is not a trivial task, but still help
in this regard may help many other fellow users besides me.
Aside from telling you to read all the literature you can, there's not much more
help anyone can do to help you. You haven't described very well what your
system is. What kind of functional groups are in your ligand? If the
functional groups are shared with existing parameters, then you'll have a rather
easy time constructing a topology. What type of metal ion is it? If you're
dealing with a transition metal, using a standard MM force field may not work
very well. Note the "Exotic Species" heading on the page you quoted above.
-Justin
Thanks in advance
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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