[gmx-users] Invalid order for directive system
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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