Re: 5' terminal issues with parmbsc0, feature or defect?
(queries by Spasic and Hopkins)
> I think I might have found an error in how some of the dihedrals are
> assigned in the frcmod.parmbsc0 file. Specifically, I think that in the
> 5'-end nucleotides these two dihedrals are not assigned correctly:
> 1. H5T-O5'-C5'-C4' or HO-OH-CI-CT (in atom types) is assigned to the
> general dihedral X-CI-OH-X while it should be assigned to the
> HO-OH-CI-CT type (analogous to HO-OH-CT-CT type in param99)
> 2. O4'-C4'-C5'-O5' or OS-CT-CI-OH (in atom types) is assigned to the
> general type X-CT-CI-X instead of OS-CT-CI-OH (analogous to the
> OS-CT-CT-OH type in param99).
> To correct this I think that the following lines should be added to the
> frcmod.parmbsc0 file:
> HO-OH-CI-CT 1 0.16 0.0 -3.
> HO-OH-CI-CT 1 0.25 0.0 1.
> OS-CT-CI-OH 1 0.144 0.0 -3.
> OS-CT-CI-OH 1 1.175 0.0 2.
There are two differences in parmbsc0 from ff99; (#1) is the 5' terminal
HO-OH-CT-CT which is assigned a 3-fold torsion but misses an additional
1-fold torsion (and likely has little consequence but I have to test this)
and (#2) what seems like a bigger issue is that all of the O5'-C5'-C4'-O4'
are now 3-fold torsions and lack the characteristic gauche anomeric
O-C-C-O 2-fold term.
However, the frcmod.parmbsc0 is "correct" despite the differences from
ff99 as it exactly reproduces Table 3 from the paper of Perez et al.
Biophys J 92, 3817-3829 (2007). For the latter change on the O-C-C-O the
methods describes the change as:
"In principle, although any dihedral angles(s) can be used to fit a
torsion, we chose to follow the standard nomenclature using the
O3'-P-O5'-C3' and O5'-C5'-C4'-C3' atoms to respresent alpha and gamma
dihedrals. This differs slightly from the original parm99 force field,
where the gamma is defined by the O5'-C5'-C4'-O4' atoms using the smae
set of atom types (OS-CT-CT-OS) as the sugar ring torsion
O4'-C4'-C3'-O3' and all other anomeric torsions. To avoid altering
other conformational profiles (such as that of sugar repuckering) a new
atom type (CI) was introduced and assigned to C5'. Defining a new atom
type for the C5' make intuitive sense because it is expected that the
O5'-C5'-C4'-O4' anomeric torsion, adjacent to the phosphorous, should be
distinct from the standard (OS-CT-CT-OS) anomeric torsion."
For the first difference from ff99 we/I will have to test the
implications, however as mentioned since this is only the terminal
hydroxyl I am not particularly worried; the change from ff99 was likely
unintentional. For the second difference, this is intentional and adding
back in the ff99 parameters for this torsion would make the force field no
longer parmbsc0 since the torsions gamma (O5'-C5'-C4'-C3') and *
(O5'-C5'-C4'-O4') are coupled via the sugar...
O5'
\
C5' O4'
gamma \ */ \
C4' C1'
| |
C3'----C2'
--tec3
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Received on Tue Apr 05 2011 - 10:00:03 PDT
