Vanessa Oklejas wrote:
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
you need to add the -type flag
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.)
g_dih is gromos specific. sorry.
(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
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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