[AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file

From: Alex Spasic <aleksspasic11.gmail.com>
Date: Tue, 21 Dec 2010 12:01:18 -0500


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.

Please let me know if this is correct.

Alex Spasic

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Received on Tue Dec 21 2010 - 09:30:02 PST
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