[gmx-users] Error using g_dih: Fatal error: Dihedral around 19, 21 not found in topology

[Vanessa Oklejas]

Hi All,

I would like to plot  dihedral angles of a protein over a trajectory, 
but I can't seem to get any of the analysis programs to work for me.

For example, > g_dih -f confout_mod.pdb


		Reading file topol.tpr, VERSION 3.1.4 (single precision)
		Found 314 phi-psi combinations
		Fatal error: Dihedral around 19,21 not found in topology



Alternatively, when I run g_angle I get the following error:

		> g_angle -f confout.gro -n h_arl2.ndx -of


		Fatal error: number of index elements not multiple of 3, these can 
not be angle tripletswhen I run g_dih

		


I suspect that there are two reasons why these programs aren't working for me:

(1) I'm using AMBER force field (ffamber99) ports for GROMACS 
(http://folding.stanford.edu/ffamber/) so the residue names and 
hydrogen atom names are not the same as for other FF typically used 
for GROMACS. However, even when I change the residue names and remove 
all hydrogens to be consistent with standard GROMACS FF, I still 
get  exactly the same error as before when using the 'g_dih' program. 
( I verified that the residue and atom names were consistent with 
other GROMACS FF by using pdb2gmx on the modified PDB file.)

(2) I don't run 'g_dih' or 'g-angle' on a trajectory, but rather on a 
PDB file that represents a single snapshot corresponding to the 
simulation output (confout.gro). I have run 'g_dih' on a trajectory 
(.trr) file, but I get the same error as above. I would prefer to use 
these programs on a trajectory, but I'm afraid that the use of a 
non-standard FF (and corresponding atypical residue and H atom names) 
precludes me from doing this.

Does anybody know of a way around this?

Thanks,
Vanessa