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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