Quoting leila karami <karami.lei...@gmail.com>: > 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. >
Your output is total nonsense. Please refer to the header of the script for proper input. I suspect the problem is with the index file. You should NOT pass the entire hbond.ndx file to the script. > 3) I think that %exist should be determined for each of > donor-hydrogen-acceptor being in hbond.ndx file.Isn't it? > > It is, provided you pass proper input to the script. -Justin > -- > > Leila Karami > Ph.D. student of Physical Chemistry > K.N. Toosi University of Technology > Theoretical Physical Chemistry Group > ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists