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 <jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.