[gmx-users] "invalid order for directive atomtypes", but only one ligand

Justin Lemkul jalemkul at vt.edu
Thu Jan 8 13:56:47 CET 2015

On 1/8/15 7:52 AM, Justin Lemkul wrote:
> On 1/7/15 4:19 PM, Jonathan Saboury wrote:
>> Hello all,
>> I'm getting an error when running grompp, "invalid order for directive
>> atomtypes".
>> I used to get this error whenever there were two or more additional .itp's
>> for ligands. This would be fixed by adding the [atomtypes] together and
>> deleting dupicates.
>> This case however there is only one ligand I am adding, so no idea where I
>> should concatenate the [atomtypes].
>> Getting error:
>> ---
>> Fatal error: Syntax error - File biotin_GMX.itp, line 3
>> Last line read: '[ atomtypes ]'
>> Invalid order for directive atomtypes
>> ---
>> Commands: http://pastebin.com/raw.php?i=FWA2W2Dd
>> Zip of all files (2.7MB): http://ge.tt/35Gex882/v/0
> You haven't provided system.top, which is where the problem would become
> evident.  There's nothing wrong with biotin_GMX.itp itself, but however it is
> being #included in system.top must be wrong.  A ligand that introduces new
> [atomtypes] must be #included after the parent force field, and prior to any
> [moleculetype] definition.  Force field-level directives must all appear before
> any molecule-level directives.

Correction - system.top is there, I just missed it because your .zip archive 
flooded my directory with stuff.  Please never upload a flat archive like that; 
always put files in a single directory and compress that...it's annoying for 
people trying to help you to have to clean up afterwards.

The #include statement is simply in the wrong place, as I suspected.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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