Ah! Thanks Justin, I just need extra coffee. Required file was not in working directory.
On Sun, Dec 20, 2015 at 9:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/20/15 4:13 PM, gromacs query wrote: > >> Hi All >> >> I have a modified base in normal DNA chain. Thus I added that residue in >> rtp file and updated residuetypes.dat as well (CHARMM36). When I use >> pdb2mx >> with -ter interactive mode then it wrongly identifies the ending terminal >> at the residue just before the modified base. e.g. >> >> >> : >> : >> TER >> DC (169th residue) >> DT >> DG (so on......) >> DC (189th residue) >> AX (moldified 190th residue) >> . >> . >> DA >> DG >> TER >> : >> : >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Warning message: >> >> Identified residue DC169 as a starting terminus. >> Warning: Residue AX190 in chain has different type (Other) from starting >> residue DC169 (DNA).. >> >> More than 5 unidentified residues at end of chain - disabling further >> warnings. >> Identified residue DC189 as a ending terminus. >> 8 out of 8 lines of specbond.dat converted successfully >> Select start terminus type for DC-169 >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> So its wrongly identifying DC as ending terminal. Not sure what else needs >> to be modified as residuetypes.dat has been updated too in my local >> directory. I dont have any new type of connection between modified base >> and >> normal base. >> >> > Simply put, this is the function of residuetypes.dat and if you have > altered it, either your modification is incorrect or the file is not in the > working directory. > > -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.