Hi Nagaraju (and Mark),
The pH is not defined for a single molecule (protein). The pH and the
pKa values of the side chains couple to the actual protonation states
by probabilities, ergo statistical distributions. You can set up a
simulation according to some reference pH in relation to the pKa
values of side chains, but it will not be 'at a certain pH'.
If you meant constant-pH simulations, that's yet another thing and
there are several posts about it in the archive.
Cheers,
Tsjerk
On 7/4/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Dear gmx users,
> Dear Mark thank you very much for your
> suggestion. I would like to do MD simulation at
> perticular pH.
This requires an implicit solvent model, which GROMACS doesn't do, and so
no force field for GROMACS is fit to work with an implicit solvent model
anywhere else either.
> I think that in AMBER it is
> possible but I have some problems regarding
> lipid bilayer parameters. Because of this I
> would like to convert gromacs lipid parameters
> to AMBER parameters. Is any formula to convert
> gromacs to amber parameters.
> I am able to convert gromacs file format
> to AMBER file format. My question is
> conversion of parameters (force
> constant, phi values, bond lenths,
> dihedral parameters etc..)
You could do this, but it won't work and nobody will spend time helping
you to do it. Force fields are parameterized to reproduce some
experimental values under various conditions. You're proposing to change
those conditions radically. You need to find some lipid parameters
suitable for your problem conditions. I'd also suggest doing some more
background reading on molecular dynamics, since this is pretty basic
stuff.
Mark
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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