[AMBER] parm10 and PARMCHK.DAT Atom Types

From: Pye, Aaron Wesley via AMBER <amber.ambermd.org>
Date: Sat, 10 Aug 2024 10:10:04 -0230

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 - 06:00:01 PDT