jalemkul at vt.edu
Thu Dec 5 18:03:30 CET 2013
On 12/5/13 11:50 AM, Steven Neumann wrote:
> Thanks I did it. However I got an error:
> Invalid order for directive exclusions
> My topology:
> [ defaults ]
> ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
> [ atomtypes ]
> ;name at.num mass charge ptype C6 C12
> ; Include Tube topology
> #include "tube.itp"
> ; Include Position restraint file of ligand
> #ifdef POSRES_TUB
> #include "posre_tube.itp"
> [ system ]
> ; Name
> [ molecules ]
> ; Compound #mols
> TUBE 1
> whre tube.itp
> [ moleculetype ]
> ; Name nrexcl
> TUBE 3
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 1 TUB rtp TUB q 0.0
> [ exclusions ]
> I do not have any bonds dihedrals or angles...
That's an essential piece of information that you hadn't shared yet. Exclusions
are based on bonded geometry. If you don't have bonds, exclusions won't work.
If there are no bonds, the only option is energygrp-excl, otherwise you need to
define bonds between the beads. If the configuration is fully restrained, then
the bonded parameters should matter very little.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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