Claus Valka wrote:
Dear Sir,
Thank you very much for your immediate responce.
In order for my text file to succeed it should have
the following format :
a C1 C2 C3 C4
a C5 C6 C7 C7
.
.
.
q
The first line says that we want the atoms with names
C1 C2 C3 C4 (depending on the names according to one's
system).
The last line is also very important because is says
to the make_ndx command to save and quit (something
also that I hadn't included in my file and as a result
the command was running without exiting, yet with the
'a' in front I saw that it had created the indexes I
wanted).
The output for the first three quadraplets is the
following :
[ C1_C4_C7_C10 ]
1 4 7 10 456 459 462 465 911 914 917
920 1366 1369 1372
1375 1821 1824 1827 1830 2276 2279 2282 2285 2731 2734
2737 2740 3186 3189
3192 3195 3641 3644 3647 3650 4096 4099 4102 4105 4551
4554 4557 4560 5006
5009 5012 5015 5461 5464 5467 5470 5916 5919 5922 5925
6371 6374 6377 6380
6826 6829 6832 6835
[ C4_C7_C10_C13 ]
4 7 10 13 459 462 465 468 914 917 920
923 1369 1372 1375
1378 1824 1827 1830 1833 2279 2282 2285 2288 2734 2737
2740 2743 3189 3192
3195 3198 3644 3647 3650 3653 4099 4102 4105 4108 4554
4557 4560 4563 5009
5012 5015 5018 5464 5467 5470 5473 5919 5922 5925 5928
6374 6377 6380 6383
6829 6832 6835 6838
[ C7_C10_C13_C16 ]
7 10 13 16 462 465 468 471 917 920 923
926 1372 1375 1378
1381 1827 1830 1833 1836 2282 2285 2288 2291 2737 2740
2743 2746 3192 3195
3198 3201 3647 3650 3653 3656 4102 4105 4108 4111 4557
4560 4563 4566 5012
5015 5018 5021 5467 5470 5473 5476 5922 5925 5928 5931
6377 6380 6383 6386
6832 6835 6838 6841
From the online gromacs manual the output I think
should be :
[ C1_C4_C7_C10 ]
1 4 7 10
456 459 462 465
911 914 917 920
...
... and so on
Is this really necessary?
Index files do not use whitespace to delimit subgroups of indices.
You're getting 64 indices because you have 16 identical polymers and
you're asking make_ndx for a set than spans across residues. I expect
that in asking for "quadruplets" g_angle requires that they be in
separate index groups, but I've never used g_angle. Try your above input
file after adding commands to restrict the atom selection to only one of
the polymers and then try g_angle again.
Mark
I tried to calculate the dihedral distribution for the
first quadraplet and it was calculated without any
error.Can I choose all the quadraplets after the
command :
g_angle -f traj.xtc -s topol.tpr -n index_created.ndx
-b 0 -e (last frame) -type dihedral -od output.xvg
Thank you once again,
Nikos
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