*** /Users/carlo/Downloads/gromacs-4.6.5/src/tools/gmx_rmsdist.c	2013-11-08 11:09:33.000000000 +0000
--- ../src/tools/gmx_rmsdist.c	2014-04-08 15:55:05.000000000 +0100
***************
*** 327,333 ****
                      if (bEquiv)
                      {
                          /* set index for matching atom */
!                         noe_index[j] = groupnr;
                          /* skip matching atom */
                          i = j;
                      }
--- 327,333 ----
                      if (bEquiv)
                      {
                          /* set index for matching atom */
!                         noe_index[i] = groupnr;
                          /* skip matching atom */
                          i = j;
                      }
***************
*** 345,351 ****
                     This is supposed to cover all CH3 groups and the like */
                  anmi   = *atoms->atomname[index[i]];
                  anmil  = strlen(anmi);
!                 bMatch = i < isize-3 && anmi[anmil-1] == '1';
                  if (bMatch)
                  {
                      for (j = 1; j < 3; j++)
--- 345,351 ----
                     This is supposed to cover all CH3 groups and the like */
                  anmi   = *atoms->atomname[index[i]];
                  anmil  = strlen(anmi);
!                 bMatch = i <= isize-3 && anmi[anmil-1] == '1';
                  if (bMatch)
                  {
                      for (j = 1; j < 3; j++)
***************
*** 648,654 ****
          "equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
          "a set of equivalent atoms specified as residue number and name and",
          "atom name; e.g.:[PAR]",
!         "[TT]3 SER  HB1 3 SER  HB2[tt][PAR]",
          "Residue and atom names must exactly match those in the structure",
          "file, including case. Specifying non-sequential atoms is undefined."
  
--- 648,654 ----
          "equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
          "a set of equivalent atoms specified as residue number and name and",
          "atom name; e.g.:[PAR]",
!         "[TT]HB* 3 SER  HB1 3 SER  HB2[tt][PAR]",
          "Residue and atom names must exactly match those in the structure",
          "file, including case. Specifying non-sequential atoms is undefined."
  
***************
*** 788,808 ****
  
      /*do a first step*/
      natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
! 
      do
      {
          calc_dist_tot(isize, index, x, ePBC, box, d, dtot, dtot2, bNMR, dtot1_3, dtot1_6);
  
          rmsnow = rms_diff(isize, d, d_r);
          fprintf(fp, "%g  %g\n", t, rmsnow);
      }
      while (read_next_x(oenv, status, &t, natom, x, box));
      fprintf(stderr, "\n");
  
      ffclose(fp);
  
-     teller = nframes_read(status);
- 
      close_trj(status);
  
      calc_rms(isize, teller, dtot, dtot2, mean, &meanmax, rms, &rmsmax, rmsc, &rmscmax);
--- 788,807 ----
  
      /*do a first step*/
      natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
!     teller=0;
      do
      {
          calc_dist_tot(isize, index, x, ePBC, box, d, dtot, dtot2, bNMR, dtot1_3, dtot1_6);
  
          rmsnow = rms_diff(isize, d, d_r);
          fprintf(fp, "%g  %g\n", t, rmsnow);
+         teller++;
      }
      while (read_next_x(oenv, status, &t, natom, x, box));
      fprintf(stderr, "\n");
  
      ffclose(fp);
  
      close_trj(status);
  
      calc_rms(isize, teller, dtot, dtot2, mean, &meanmax, rms, &rmsmax, rmsc, &rmscmax);