Dear Justin Thank you so much for help.
I used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat. this file is as follows: # Donor Acceptor % Exist. 5.478 NGL1 N NGL1 H2 0.040 LYP2 HB2 LYP2 HG1 0.040 LYP2 O GLY3 H 6.158 GLN5 N GLN5 CA 0.040 GLN5 C VAL6 N 0.040 VAL6 3HG2 VAL6 O 0.320 ARG7 HD2 ARG7 HE 0.040 PHE8 HA PHE8 HB1 8.517 PHE8 C SER9 N 1.439 ASN10 CA ASN10 CB 0.600 ASP11 HA ASP11 HB1 0.040 GLN12 HB2 GLN12 HG1 0.440 THR13 CB THR13 CG2 3.199 ILE14 HB ILE14 1HG2 0.800 GLU15 H GLU15 HA 3.798 LEU16 H LEU16 HA 0.040 LEU16 3HD2 LEU16 O 0.040 GLU17 OE2 GLU17 O 2.279 LYP18 HD2 LYP18 HE1 30.508 LYP19 HB1 LYP19 CG 23.231 LYP19 C PHE20 N 0.840 PHE20 HZ PHE20 HE2 0.040 GLU21 HG1 GLU21 CD 0.480 THR22 2HG2 THR22 OG1 4.518 GLN23 HG2 GLN23 OE1 0.360 LYP24 CG LYP24 HG2 0.120 TYR25 N TYR25 CA 0.080 TYR25 CE2 TYR25 CD2 1.519 LEU26 CD1 LEU26 2HD1 10.716 SER27 HB1 SER27 OG 3.958 PRO28 HB2 PRO28 HA 0.120 PRO29 CA PRO29 C 0.440 GLU30 OE1 GLU30 C 11.955 17.193 NGL1 N 5.718 GLU30 N 7.837 SER27 OG 1.279 SER27 N 6.078 LEU26 N 0.040 TYR25 OH 0.080 TYR25 N 49.100 LYP24 NZ 89.204 LYP24 N 7.917 GLN23 NE2 25.590 GLN23 N 73.051 THR22 OG1 1.719 THR22 N 93.882 GLU21 N 1.839 PHE20 N 0.200 LYP19 NZ 0.040 I have some question: 1) when I used g_hbond for obtaining hbond.ndx and hbmap.xpm and hbond.log file, I selected two groups(1- protein nad 2- dna).In hbond.log and hbond.ndx file there are acceptors and donors belonging to both of protein and dna, while in my summary_HBmap.dat file both of donors and acceptors only belongs to protein. is there problem? 2) at the end of this file, there are only donors. what is means of %exist for these donors. This file should give me existence of each hbond during my trajectory and not donors. 3) I think that %exist should be determined for each of donor-hydrogen-acceptor being in hbond.ndx file.Isn't it? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group
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