Hi Aaron,
What are the definitions for these atom types (CM and CS) per the
parm10.dat (ff14SB) forcefield?
Cheers,
Kyle
On Sat, Aug 10, 2024 at 10:11 Pye, Aaron Wesley via AMBER <amber.ambermd.org>
wrote:
> Hi All,
>
> I am currently preparing a modified uracil nucleotide for simulation, and
> I'm using antechamber and parmchk2 to assign atom types and parameters.
> Antechamber assigned CM to C5 and C6 of the pyrimidine ring (atoms 25 and
> 24 in the attached mol2), so I changed these atom types to CS to better
> match definitions in parm10.dat. Now when running parmchk2, I get an error
> saying 'Atom type of CS does not exist in PARMCHK.DAT', however using CM
> for C5 and C6 doesn't give this error. Is there something I'm missing?
> Alternatively, CM and CS seem to have all the same values (in bond lengths,
> dihedrals, etc.) in parm10.dat, so would there be any issues with just
> using CM?
>
> Thanks,
> Aaron
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Received on Sat Aug 10 2024 - 07:00:02 PDT
