Thank you Justin,
that makes sense, thank you for help. However, I am struggling with the
rest, due to lacking documentation & examples. Like Alex said, this
web-page http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA is
outdated, but there is no new version of it available... Or at least I
am not finding it (and I have noticed that people on the list have asked
questions similar to mine, but there were no answers to any of my
questions, sadly).
mk_angndx -s h3_md.tpr -n h3_ANGLE.ndx -type dihedral
is what I now have done, and my next steps should be the following, I guess,
trjconv -s h3_md.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0
but I do not have a trr file because mk_angndx does not generate it
(unlike the old documentation command angle) and again, my tpr file
contains waters, not just the molecule of interest that I have in my
.gro file. I also do not understand the difference between the
dangle.ndx file and covar.ndx file... What is resized.gro? It would be
really helpful to write out those explanations in documentation and
perhaps give a more realistic example because this really becomes
frustrating.
Thanks for your time & help, it is very much appreciated.
Anna
On 27/02/17 19:58, Justin Lemkul wrote:
On 2/27/17 9:55 PM, Anna Vernon wrote:
Thanks Justin,
but I did use this command, which is supposed to be dihedral:
g_angle -f h3_nowater.gro -n h3_ANGLE.ndx -or h3_ANGLE.trr -type
dihedral
Sure, but g_angle is only going to give you the options presented to
it in the index file. If those groups were created incorrectly (note
my comments were about mk_angndx, not g_angle) then you have to create
them properly. You can't get dihedrals from valence angles :)
-Justin
thanks
A
On 27/02/17 19:35, Justin Lemkul wrote:
On 2/27/17 9:29 PM, Anna Vernon wrote:
Thanks Alex.
tried the new syntax, below the output of g_angle, which did not
get any
easier... Хрень осталась...)))
Group 0 (UB_th=108.4_297.062f) has 36 elements
Group 1 (UB_th=108.9_384.092f) has 30 elements
Group 2 (UB_th=109.7_794.962f) has 6 elements
Group 3 (UB_th=111.5_376.562f) has 6 elements
Group 4 (UB_th=110.1_221.752f) has 36 elements
Group 5 (UB_th=109.0_297.062f) has 33 elements
Group 6 (UB_th=109.5_430.952f) has 36 elements
Group 7 (UB_th=113.5_585.762f) has 12 elements
Group 8 (UB_th=121.0_376.562f) has 12 elements
Group 9 (UB_th=119.5_351.462f) has 24 elements
Group 10 (UB_th=124.0_669.442f) has 12 elements
Group 11 (UB_th=112.5_167.362f) has 12 elements
Group 12 (UB_th=121.0_669.442f) has 15 elements
Group 13 (UB_th=109.5_276.142f) has 30 elements
Group 14 (UB_th=107.0_418.402f) has 12 elements
Group 15 (UB_th=112.2_365.682f) has 6 elements
Group 16 (UB_th=109.5_271.122f) has 6 elements
Group 17 (UB_th=109.5_271.122f) has 12 elements
Group 18 (UB_th=110.0_365.682f) has 3 elements
Group 19 (UB_th=111.0_292.882f) has 6 elements
Group 20 (UB_th=112.2_338.902f) has 3 elements
Group 21 (UB_th=111.0_359.822f) has 6 elements
Group 22 (UB_th=108.0_401.662f) has 6 elements
Group 23 (UB_th=110.1_288.702f) has 6 elements
Group 24 (UB_th=115.2_443.502f) has 6 elements
Group 25 (UB_th=107.5_433.462f) has 6 elements
Group 26 (UB_th=120.0_383.252f) has 12 elements
Group 27 (UB_th=120.0_334.722f) has 36 elements
Group 28 (UB_th=120.0_251.042f) has 60 elements
Group 29 (UB_th=110.1_279.742f) has 18 elements
Group 30 (UB_th=105.8_351.462f) has 3 elements
Group 31 (UB_th=112.1_343.092f) has 6 elements
Group 32 (UB_th=116.5_418.402f) has 3 elements
Group 33 (UB_th=122.5_627.602f) has 3 elements
Group 34 (UB_th=120.0_418.402f) has 6 elements
Group 35 (UB_th=120.0_192.462f) has 3 elements
These are Urey-Bradley angles with the given equilibrium angles and
force
constants. If you're using mk_angndx to create the index group, you
want
"-type dihedral" instead of "-type angle" (which is the default).
-Justin
On 27/02/17 16:04, Alex wrote:
I think you might be referring to the 2010 version of the online
manual (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA), which
is pretty
outdated. A lot of syntax seems to be changing fairly rapidly, so
хрень
like this is to be expected. ;)
The current manual points to gmx angle, gmx covar and, gmx anaeig for
covariance analysis, and for those the updated help pages are
separate:
http://manual.gromacs.org/programs/gmx-angle.html
http://manual.gromacs.org/programs/gmx-covar.html
http://manual.gromacs.org/programs/gmx-anaeig.html
Alex
On Mon, Feb 27, 2017 at 3:44 PM, Anna Lappala
<lappala.a...@gmail.com>
wrote:
Dear Gromacs users,
The documentation on Dihedral PCA analysis is confusing.
Firstly, the links are redirecting to the main gromacs page
which does
not help because one needs to search for the specific commands
from there.
Secondly, -s option does not work in step 2: invalid command line
argument
"-s".
Thirdly, my tpr file contains water which I do not want to
include in the
analysis, how can I change that?
.ndx file output produced by mk_angndx is a mess- first line, for
example,
is [UB_th=108.4_297.062f]
I need a small number of dihedrals, so I could write the file
myself but
there again is no clear explanation how to do it: the [foo] 1 2 3
4 example
could be expanded- do I use "dihedrals" instead of foo? Or
filename? Or
molecule name?
Finally, I would really appreciate it if someone could give an
explanation
or a clear example of how this works, for a simple system or a
protein,
because documentation is unclear to me.
Kind regards,
Anna
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