[gmx-users] help on converting charmm/cgenff parameters to gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 7 14:22:12 CEST 2011

On 7/04/2011 9:38 PM, Peter C. Lai wrote:
> Ok here's a minor? problem I'm having with dihedrals.
> Apparently grompp won't read H-H dihedrals such as:
> HGA2   CG321  CG321  HGA2           9       0.00    0.92048 3 ;LIPID alkane
> HGA2   CG321  CG331  HGA3           9       0.00    0.66944 3 ;PROT rotation barrier in ethane
> (the lipid equiv would be: HAL2 CTL2 CTL2 HAL2)
> it only seems to work if I use
> X CG321 CG321 X
> but that always seems a bit too broadspectrum...
> I'm not using heavy H or anything, just a normal pdb2gmx and normal grompp
> but it complains about the H-H dihedrals as "No default Proper Dih. types"...
> Any ideas?

So the relevant hydrogen atoms do not have type HGA2 or HGA3, or you're 
not using the right files. Perhaps the error message says what line of 
the .itp is causing problems...


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