it was wrong i make new index that contain Non-Protein group. my problem fix!
tnx On Mon, Jul 25, 2016 at 12:08 AM, masoud keramati <keramati.ma3...@gmail.com > wrote: > tnx Dr.Lemkul > > yes the problem was in the tc-grps. > tc-grps = Protein Non-Protein > and there is no Non-Protein group in index file. > it's true that i use System for tc-grps? > > On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 7/24/16 3:17 PM, masoud keramati wrote: >> >>> Hi all >>> >>> i have a protein with six chain. >>> i create an index file that include each chain (chA chB ..) >>> in mdp file i define energy groups such that: >>> energygrps = chA chD >>> >>> for grompp i used this command: >>> gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr >>> >>> but i got this error: >>> "Group Non-Protein referenced in the .mdp file was not found in the index >>> file. >>> Group names must match either [moleculetype] names or custom index group >>> names, in which case you must supply an index file to the '-n' option >>> of grompp " >>> >>> what's wrong with this?! >>> >>> >> You have some setting that uses Non-Protein but you haven't got that in >> your index file. Check tc-grps as the most likely culprit. If your index >> file *only* contains the chains that you've specified, then you're going to >> encounter problems. In general, add groups that you need and leave the >> default groups (System, Protein, Non-Protein, etc.) in place for ease of >> use. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> 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.