Dear Justin<br><br>Thank you so much for help.<br><br>I used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat.<br>this file is as follows:<br><br># Donor Acceptor % Exist. <br>
5.478 <br> NGL1 N NGL1 H2 0.040 <br> LYP2 HB2 LYP2 HG1 0.040 <br> LYP2 O GLY3 H 6.158 <br>
GLN5 N GLN5 CA 0.040 <br> GLN5 C VAL6 N 0.040 <br> VAL6 3HG2 VAL6 O 0.320 <br> ARG7 HD2 ARG7 HE 0.040 <br>
PHE8 HA PHE8 HB1 8.517 <br> PHE8 C SER9 N 1.439 <br> ASN10 CA ASN10 CB 0.600 <br> ASP11 HA ASP11 HB1 0.040 <br>
GLN12 HB2 GLN12 HG1 0.440 <br> THR13 CB THR13 CG2 3.199 <br> ILE14 HB ILE14 1HG2 0.800 <br> GLU15 H GLU15 HA 3.798 <br>
LEU16 H LEU16 HA 0.040 <br> LEU16 3HD2 LEU16 O 0.040 <br> GLU17 OE2 GLU17 O 2.279 <br> LYP18 HD2 LYP18 HE1 30.508 <br>
LYP19 HB1 LYP19 CG 23.231 <br> LYP19 C PHE20 N 0.840 <br> PHE20 HZ PHE20 HE2 0.040 <br> GLU21 HG1 GLU21 CD 0.480 <br>
THR22 2HG2 THR22 OG1 4.518 <br> GLN23 HG2 GLN23 OE1 0.360 <br> LYP24 CG LYP24 HG2 0.120 <br> TYR25 N TYR25 CA 0.080 <br>
TYR25 CE2 TYR25 CD2 1.519 <br> LEU26 CD1 LEU26 2HD1 10.716 <br> SER27 HB1 SER27 OG 3.958 <br> PRO28 HB2 PRO28 HA 0.120 <br>
PRO29 CA PRO29 C 0.440 <br> GLU30 OE1 GLU30 C 11.955 <br> 17.193 <br> NGL1 N 5.718 <br>
GLU30 N 7.837 <br> SER27 OG 1.279 <br> SER27 N 6.078 <br> LEU26 N 0.040 <br>
TYR25 OH 0.080 <br> TYR25 N 49.100 <br> LYP24 NZ 89.204 <br> LYP24 N 7.917 <br>
GLN23 NE2 25.590 <br> GLN23 N 73.051 <br> THR22 OG1 1.719 <br> THR22 N 93.882 <br>
GLU21 N 1.839 <br> PHE20 N 0.200 <br> LYP19 NZ 0.040 <br clear="all">
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</font></font><br>I have some question: <br><br>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?<br>
<br>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.<br><br>3) I think that %exist should be determined for each of donor-hydrogen-acceptor being in hbond.ndx file.Isn't it?<br>
<br clear="all"><br>-- <br><pre style="font-family: arial,helvetica,sans-serif;">Leila Karami<br>Ph.D. student of Physical Chemistry<br>K.N. Toosi University of Technology<br>Theoretical Physical Chemistry Group</pre><br>