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From: tarak karmakar <tarak20489.gmail.com>

Date: Wed, 13 Jan 2016 23:12:35 +0530

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.
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Wed Jan 13 2016 - 10:00:03 PST

Date: Wed, 13 Jan 2016 23:12:35 +0530

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:

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Received on Wed Jan 13 2016 - 10:00:03 PST

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