I read over the comments on the mailing list, and found some ways to
make the grompp warnings go away while using ACE or NAC terminii, but
was not able to understand what the most proper way to do things was.
The missing dihedrals are because the CH3 is opls_135 (ACE) or
opls_242 (NAC) which are both type "CT" where all other CA atoms are
of type CT_2.
Based on the following lines from ffoplsaabon.itp:
CA N C CT 3 30.28798 -4.81160 -25.47638
0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3
CT C N CT 3 30.28798 -4.81160 -25.47638
0.00000 0.00000 0.00000 ; amides - V1 changed to 2.3
CT_2 C N CT_2 3 30.28798 -4.81160 -25.47638
0.00000 0.00000 0.00000 ; peptide - V1 changed to 2.3
It seems reasonable to me that a CT-C-N-CT_2 RB-dihedral be created
with the same values. Therefore I have added the following lines:
[ dihedraltypes ]
; i j k l func coefficients
CT C N CT_2 3 30.28798 -4.81160 -25.47638
0.00000 0.00000 0.00000 ; For ACE/NAC (Sept2006) adapted from
CT_2-N-C-CT_2 parameters with original comment="peptide - V1 changed
to 2.3"
Added to my topology file after #include "ffoplsaa.itp" and before [
moleculetype ]
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