[gmx-users] spurious dihedral warnings

[mernst at tricity.wsu.edu]

Hello,

I am using gromacs 3.3.

I have a line in my .itp file that looks like this before I actually define a different
"B" state:

43 amber99_40      2    8oG     N9     43      0.111      14.01    amber99_40 0.111 14.01

I can generate a .tpr file with no warnings. However, when I give it a different partial
charge in the "B" state:

43 amber99_40      2    8oG     N9     43      0.111      14.01    amber99_40 0.0577 14.01

Then I get the following warning from grompp:

WARNING 1 [file "trimer_A.itp", line 942]:
  No default Proper Dih. types for perturbed atoms, using normal values

Line 942 looks like this:

41    43    44    58     1    nucleic_imp_10

The warning persists even when I change it to this:

41    43    44    58     1    nucleic_imp_10 nucleic_imp_10

Using gmxcheck, the only difference I find between the warning-bearing and warning-free
cases is the different partial charge in the "B"-state on atom 43.

Further, it turns out that I can also trigger the warning by changing the mass of the
atom in the "B"-state.

In http://www.gromacs.org/pipermail/gmx-users/2006-January/019269.html it seems that
Jonathan Moore has encountered this problem before, found no fix, and decided to just
ignore the warnings. I will be ignoring them too for now, but I don't like ignoring
warnings. Aren't proper dihedrals defined by the atom types involved? How could changing
the atom's partial charge or mass result in dihedral misrecognition?

Matt Ernst
Washington State University