s.neumann08 at gmail.com
Thu Dec 5 17:50:38 CET 2013
Thanks I did it. However I got an error:
Invalid order for directive exclusions
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
[ atomtypes ]
;name at.num mass charge ptype C6 C12
; Include Tube topology
; Include Position restraint file of ligand
[ system ]
[ molecules ]
; Compound #mols
[ moleculetype ]
; Name nrexcl
[ 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...
would you advise?
On Thu, Dec 5, 2013 at 3:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 12/5/13 10:28 AM, Steven Neumann wrote:
>> I guess I need to write [ exclusions ] as TUB is composed of other
>> energygrps. I have 2516 atoms, that would be difficult to write [
>> exclusions ] manually, would you recommend any script? I am not
> It's an easy loop. Every atom is excluded from all others. You just need
> to take care to not write repetitive exclusions (i.e. an exclusion of 1 2
> is the same as 2 1), but that's simple to do.
> Learning a simple scripting language is an essential skill; it will save
> you countless hours.
> 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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