[gmx-users] Re: write topology by hand

[Vitaly Chaban]

> Hi everyone,
> I had a .pdb file that was drug_enzyme complex. Drug was GOL(Glycerol) and I wrote topology file by >hand but now when I run grompp command I have this error:Fatal error:Syntax error - File ffoplsaabon.itp, >line 4Last line read:'[ bondtypes ]'Invalid order for directive bondtypes
> and I don't know how can I  do this?
> Thank you

I suppose you have too many "$include" in your topol.top. Normally if
everything was done by hand, you do not need [bondtypes] but only
[bonds] to run grompp successfully. Note, this is true if you have the
complete entries (!) (with constants) for bonds, angles, etc in your
topology.

Good luck.

Dr. Vitaly Chaban