[gmx-users] Invalid order for directive system

Justin Lemkul jalemkul at vt.edu
Thu Sep 29 17:01:25 CEST 2016

On 9/29/16 4:44 AM, Sahithya S Iyer wrote:
> Dear gmx users,
> I am trying to run a martini CG membrane protein system. The required itps
> are included in the top file --
> include "martini_v2.2P.itp"
> include "Protein.itp"
> include "martini_v2.0_lipids_all_201506.itp"
> include "martini_v2.0_ions.itp"
> The itp file has restrains for protein backbone (Protein.itp) and phosphate
> head group (martini_v2.0_lipids_all_201506.itp) of bilayer. This is
> included in the equilibration mdp file as -
> define  = -DFLEXIBLE  -DPOSRES
> When i use the grompp command to generate a tpr i get the following error -
> Fatal error:
> Syntax error - File system.top, line 6
> Last line read:
> '[ system ]'
> Invalid order for directive system
> I thought i had given the order of the itp files correct. I have looked
> though the previous answers on the same context, but it didn't rectify the
> error. Can someone please tell me where i am going wrong..

Your #include statements are out of order.  You can't introduce a molecule until 
the whole force field is defined.  It looks like you have protein parameters, 
the protein, lipid parameters, and ion parameters.  That's invalid.  The whole 
force field needs to be declared before any species can be defined within it. 
See Chapter 5 of the manual.



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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