Hi Thomas,
I am not sure I understand your arguments for the second dihedral.
This is how I understood the procedure. New atom type CI was introduced
at the C5' atom so that alpha and gamma angles would be unique, and then
they were fitted. Then all other dihedrals which contain atom C5' were
rewritten in the frcmod.parambsc0 file with the same parameters as in
param99 but with CT replaced with CI wherever C5' atom was. That way
only alpha and gamma would be changed but all other dihedrals would be
the same as in param99. However, dihedrals OS-CT-CI-OH and OS-CT-CI-OS
(OS-CT-CT-OH and OS-CT-CT-OS in param99) were not included, so these are
now (unintentionally) read as the general type X -CT-CI-X.
Best regards,
Alex
On 04/05/2011 12:31 PM, Thomas Cheatham III wrote:
> 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
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 05 2011 - 12:30:02 PDT
