On 12/12/14 12:52 PM, xy21hb wrote:
Dear all, I am introducing a residue named ABC into AMBER03 force field. I built up the aminoacids.rtp and aminoacids.hdb file, but when I pdb2gmx, it gives, " Atom HB1 not found in rtp database in residue ABC, it looks a bit like HB " I am pretty sure I use HB instead of HB1, and there is no atom called HB1 in any of the above-mentioned files.(including .pdb for pdb2gmx) then I changed my HB to HB1, it gives similar error, " Atom HB11 not found in rtp database in residue ABC, it looks a bit like HB1 " It seems that pdb2gmx is appending the name with "1". Anyone knows why that is?
Probably due to the .hdb entry - if multiple H are to be built on a single heavy atom, numbers are appended so they have unique names. But to take the guesswork out, you'll need to provide the exact text of the .rtp and .hdb files.
-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.
