Dear CHARMM Users,
I am using the CHARMM36 FF for DNA and RNA. par_all36_na.prm (downloaded from the sticky on this forum)
I noticed a discrepancy in the parameters for the LJ of carbon atoms in the sugars. The topology files identify these carbons as either CN7, or CN7B.
These are Sp3 carbons with a single hydrogen. The parameters for these atom types are given:
CN7 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
CN7B 0.0 -0.02 2.275 0.0 -0.01 1.90 !equivalent to protein CT1
When I examine the protein parameters I notice they are not equivalent to CT1, but CT.
This seems odd considering CT1 is an Sp3 carbon with a single hydrogen, the same as CN7 and CN7B.
CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 !
CT1 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane, 4/07, viv and adm jr.
However, they do match the CT1 atom type from par_all22_prot.prm
CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
My question is, should I use the parameters as given or do I need to update the nucleotide parameters to the CHARMM36 protein CT1 found in par_all36_prot.prm?