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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Received on Wed Jan 13 2016 - 06:30:04 PST
