[gmx-users] Re: write topology by hand

Vitaly Chaban vvchaban at gmail.com
Sat Jun 12 19:52:07 CEST 2010

> 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

Good luck.

Dr. Vitaly Chaban

More information about the gromacs.org_gmx-users mailing list