[gmx-users] Re: Conversion of gromacs parameters to AMBER parameters

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 4 21:42:16 CEST 2007

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.



On 7/4/07, Mark Abraham <mark.abraham at anu.edu.au> 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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