[gmx-users] exclusions

[Justin Lemkul]

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"
> #endif
>
>
> [ system ]
> ; Name
> Protein
>
> [ 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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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