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

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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