onetwo wrote:
Thanks Justin for the help,
I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.
Mangnese may have topology similar to Magnesium 2+, What I found is that
Assuming a transition metal "may" be similar to another species is probably a
pretty poor assumption. Prepare for lots of criticism if you proceed with that
thought.
I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I
calculate the nonbond_params for ffG43a1nb.itp.
Refer to the other GROMOS papers for how they derive parameters for small
molecules. I've never seen a demonstration of transition metal parameterization
under these force fields, though. Perhaps you should be using an AMBER force
field that contains Mn2+. Any particular reason you think you need GROMOS?
For both the other two ligands which contains phosphate and enol groups,
I was able to create topology using PRODRG server.
Please pay careful attention to the second paragraph here:
http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips
-Justin
Regards
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
>
>
-- ========================================
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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========================================
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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