[gmx-users] Using ACE and NAC with oplsaa

[chris.neale at utoronto.ca]

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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