[gmx-users] write topology by hand

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 12 19:06:10 CEST 2010

Quoting you zou <zou.you at live.com>:

> 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?

Have you consulted the manual for required topology format?  How about the
Gromacs website?  You probably would have found this:


If you need specific advice, you'll need to provide the relevant snippets of the
topology (including the problematic line).


> Thank you
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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