[gmx-users] Error using g_dih: Fatal error: Dihedral around 19, 21 not found in topology
voklejas at stanford.edu
Mon Aug 7 21:38:44 CEST 2006
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?
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