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.
In gaff.dat file that is present in the following amber archive,
http://archive.ambermd.org/201111/att-0689/gaff.dat
the aforementioned numbers are there.
Could you please comment on the issue that I am facing in my simulation?
Thanks,
Tarak
On Wed, Jan 13, 2016 at 7:50 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> Similar does not mean the same. The former is apparently data for the
> nucleotide force field while GAFF is a general force field for small
> organic ligands. There may have been reasons why the dihedrals have
> been chosen to be different.
>
> Nevertheless note that none of these files are AMBER files. I guess you
> have prepared your simulation setup with acpype and are running
> simulations with Gromacs?
>
>
> On Wed, 13 Jan 2016 19:12:37 +0530
> tarak karmakar <tarak20489.gmail.com> wrote:
>
> > Dear All,
> > I have a confusion related to two dihedral parameters that are
> > present in ffbonded.itp file,
> > X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
> > X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
> >
> > the similar dihedral parameters from parm99SBgaff.dat (GAFF) file,
> > X -oh-p5-X 3 1.600 0.000 3.000
> > X -os-p5-X 3 2.400 0.000 2.000
> >
> > As you see, there is a mismatch between the periodicity (last column)
> > of the similar dihedral angle from AMBER99SB and gaff databases.
> >
> > Would anybody like to comment on this?
> > I just read an earlier discussion in the following link,
> > http://dev-archive.ambermd.org/200506/0023.html
> > But, my problem is little more than the above.
> >
> > I am currently simulating a protonated pyrophosphate ligand molecule
> > in a protein. During the heating step in NVT ensemble (within 150-200
> > ps, 200 K temp), the atoms present in the phosphate groups (P,O and
> > H) are showing bizarre bonds and angles. I tried with the higher
> > force constants (10 times than the existing one) for the above
> > mentioned dihedral angles, and then the molecule was behaving fine.
> >
> > Has anybody experienced this type of issue?
> > I appreciate any suggestions.
> >
> > Regards,
> > Tarak
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>
>
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Received on Wed Jan 13 2016 - 07:00:03 PST
