[gmx-users] g_hbond / hbmap.xpm file
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 10 14:50:51 CET 2010
shahab shariati wrote:
> Dear Erik and Justin
>
> Thanks for your time and attention.
>
> My xpm file is following state:
>
>
> /* XPM
> */
>
> /* Generated by g_hbond
> */
>
> /* This file can be converted to EPS by the GROMACS program xpm2ps
> */
> /* title: "Hydrogen Bond Existence Map"
> */
>
> /* legend: "Hydrogen Bonds"
> */
>
> /* x-label: "Time (ps)"
> */
>
> /* y-label: "Hydrogen Bond Index"
> */
>
> /* type: "Discrete"
> */
>
> static char *gromacs_xpm[] =
> {
>
> "126 40 4
> 1",
>
> " c #FFFFFF " /* "None"
> */,
>
> "o c #FF0000 " /* "Present"
> */,
>
> "- c #0000FF " /* "Inserted"
> */,
>
> "* c #FF00FF " /* "Present & Inserted"
> */,
>
> /* x-axis: 19500 19504 19508 19512 19516 19520 19524 19528 19532 19536
> 19540 19544 19548 19552 19556 19560 19564 19568
> /* y-axis: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
> 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 0 */
> " o
> o ",
> "ooooooooooooooo ooo ooooo ooooooooooooooooooooooooooooooooooooo
> ooooooooooooooooooooooooooooooooooooooooo ooooooooooooo oooooo",
> "ooo ooooooo oooooooooooo oooooooooooo
> oooooooooooooooooooooooooooooooooo ooo
> oooooooooooooooooooooooooooooooooo oooooooooooooo",
> "oooooo oo ooo oooo ooooooo oooo ooo ooooooo ooo oooooo ooo oo
> oooo o o oooooooo o ooooo oo oooo o oo oooooo oo oo o",
> " o
> o ",
> "oooooo ooooooooooooooooo oooo oo oooooooo oo ooooooooooooooo
> ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo",
> " oo oooo oo ooo o oooo oo oooooooo oooooo ooooo ooooooooooo
> oooo ooo oo o oo ooo ooooooooo ooooooooo oo ooo oooooooo",
> "
> o oo o o o ",
> " o o oooo o o
> o o o o o o ",
> "
> o o ",
> "oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo",
>
> " o o o
> o o ",
> "oooooooo ooooooooooooooooooooo o ooooooo ooo ooooo oooooooooooooo
> oooooooooo o oooooooooooooooooo o oo o ooooooooo ooooo",
>
>
> and h-bond section of .ndx file is as follows:
>
> [ hbonds_Protein -Ligand ]
> 1019 1021 1640
> 1019 1021 1643
> 1019 1021 1656
> 1013 1014 1643
> 995 997 1580
> 992 994 1580
> 992 994 1581
> 992 994 1582
> 946 949 1135
> 915 917 1580
> 915 917 1581
> 909 910 1580
> 909 910 1581
> 867 869 1212
> 777 780 1517
> 777 780 1518
> 740 742 1198
> 723 725 1231
> 720 722 1231
> 504 506 1516
> 504 506 1517
> 501 503 1516
> 103 104 1166
> 103 104 1168
> 95 97 1198
> 92 93 1174
> 92 93 1196
> 79 80 1166
> 79 80 1168
> 63 64 1835
> 32 33 1752
> 26 29 1784
> 26 29 1787
> 1791 1793 45
> 1755 1757 9
> 1627 1629 852
> 1627 1629 853
> 1597 1599 852
> 1215 1217 866
> 1215 1217 867
>
> what is your mean of reading backward .xpm? above files or ps file
> obtained from xpm2ps.
>
The first hydrogen bond listed in the .ndx file corresponds to the last line of
the .xpm file. The .xpm lines are written top-down, that is, as they appear in
the .eps file obtained from xpm2ps. The numerical indices displayed on the
y-axis of the resulting .eps file correspond to the order of the indices in the
.ndx file.
-Justin
--
========================================
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
========================================
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