Hi Hannes and Jason,
Thanks for the discussion.
To mention few points here,
1) I ran a test simulation of only the ligand in water, and the geometry is
fairly stable during the two steps equilibrations, NVT followed by NPT.
Then the next protein-ligand simulation resulted the distorted geometry of
the ligand. This is quite surprising!
2) In another set of simulation, as I said earlier, I used a force constant
of 10.46 kJ/mol/rad2 for both the dihedral angles with periodicity 3. Now,
the ligand is behaving properly, I mean without any large structural
distortions.
3) I have not done any conversion from the RB dihedrals (provided by
acpype) to the proper ones. In fact, I just collected the corresponding
dihedral parameters from gaff.dat file and used those numbers with proper
conversion (energy conversion) factors.
Currently, I am using bit older version of gromacs, version 4.5.5.
Regards,
Tarak
On Wed, Jan 13, 2016 at 10:34 PM, Hannes Loeffler <
Hannes.Loeffler.stfc.ac.uk> wrote:
> On Wed, 13 Jan 2016 11:43:47 -0500
> Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Wed, Jan 13, 2016 at 9:39 AM, tarak karmakar <tarak20489.gmail.com>
> > wrote:
> >
> > > Hi Hannes,
> > > Thanks for looking at my problem.
> > > Yes, I realized the differences by looking at other similar
> > > parameters, such as,
> > > X C C X 9 180.0 15.16700 2 ; Junmei et al,
> > > 1999 and,
> > > X -c -c -X 4 1.200 180.000 2.000
> > >
> > > Yes, I have used acepype to generate the gaff parameters and running
> > > simulation with gromacs.
> > > I avoided RB parameters that are listed in the acepype output file
> > > for some reason.
> > >
> >
> > Are you sure this is the correct thing to do? As long as the phase
> > shift angles are 0 or 180 degrees, a Fourier expansion of standard
> > "proper" dihedrals can be converted into an equivalent R-B torsion
> > function form. If this is what acpype is doing (and I don't know,
> > because I don't know the details of acpype), then "skipping" these
> > terms is definitely the wrong thing to do.
> >
> > Or am I misunderstanding you?
>
>
> I believe older versions of Gromacs didn't support the general Fourier
> series for dihedrals so converting to R-B was the only option. Newer
> versions do now so there should be not need to convert but just use the
> parameters straight from AMBER (after energy conversion of course). I
> think that is what acpype does.
>
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Received on Wed Jan 13 2016 - 10:00:03 PST
