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
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
