[gmx-users] g_rama: Dihedral not found in topology

[Lutz Maibaum]

I am getting the following warning message from g_rama, even for a simple system like a blocked Alanine dipeptide:

$ g_rama -s test.tpr -f traj.xtc
[…]
Reading file test.tpr, VERSION 4.5.1 (single precision)
Found 1 phi-psi combinations
Dihedral around 6,8 not found in topology. Using mult=3
[…]

I have attached the files required to reproduce this problem. The two backbone dihedral angles for this systems are for the atom sets (5,7,9,15) and (7,9,15,17), and both groups appear in the [ dihedrals ] section of the topology file (and also exist in the tpr file). This happens using Gromacs 4.5.1 and 4.0.7.

If you would like to reproduce this behavior, I have attached a small test set (never mind that the simulation doesn't necessarily make sense). I used the following sequence of commands:

grompp -f test.mdp -c initial.gro -p topol.top -o test.tpr
mdrun -s test.tpr 
g_rama -s test.tpr -f traj.xtc 

While the output of g_rama looks reasonable, the warning message makes me worried that I might have missed something in the topology file.

Thanks,

  Lutz



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