[gmx-users] exclusions

[Steven Neumann]

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...

would you advise?

Steven


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
>> programming
>> :(
>>
>>
> 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
>
> --
> ==================================================
>
> 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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