Hi,
Probably your best bet to debug this is to write the vector data out
as a pseudo-trajectory (vectraj) and visualize it along with the
original trajectory; something like:
parm crystal_3FBV_ion_ok.prmtop
trajin reeim.xtc
rms first :
1-1687.CA
vector A corrplane
:6,12-14-22,25-30,33-79,83-86,106-137,154-216,222-243,255-258-287-320-322,341-343-366-369,395-466-469,477-534,547-586,596-611-615,628-630-683,684-686-688,700-720-732-735-823,
840.CA
vector B corrplane
:888,896-903-957,966-1005,1016-1018-1031-1034-1036,1047-1050-1103,1104-1106-1108,1120-1140-1143,1144-1150,1152-1243,1260-1261,1265-1273,1279-1281-1289,1293-1295,1299-1346,1350-1353,1373-1375-1404,1422-1484,1489-1510,1522-1559,1554-1587-1589,1607-1610-1616-1633,1634-1636,
1662.CA
run
writedata vecA.nc vectraj A trajfmt netcdf parmout A.parm7
writedata vecA.nc vectraj B trajfmt netcdf parmout B.parm7
or if you want both vectors in the same trajectory:
writedata vecs.nc vectraj A B trajfmt netcdf parmout vecs.parm7
Hope this helps,
-Dan
On Tue, Mar 24, 2020 at 8:56 AM Antonio Amber Carlesso
<antonio.amber.carlesso.gmail.com> wrote:
>
> Dear Amber Users,
>
> I performed an angle analysis between two dimer interface defined as any
> pair of Cα atoms (example system below)
>
> [image: image.png]
>
>
> I performed this analysis with four different systems.
>
> Since the systems investigated are rotated to the right and rotated to the
> left I was expecting as output (a) positive and (b) negative angles (*i.e.*
> for example + 25-30 degrees for right hand and - 25-30 for left hand
> rotated)
>
>
>
> Do you have any idea why the value received as output is always positive?
>
>
>
> Thank you for the help!
>
>
>
> The command line used was:
>
> “
>
> #Add Modules, etc etc
>
> module load amber/16.at17
>
> $AMBERHOME/bin/cpptraj
>
>
>
> # load prmtop and trajectory
>
> parm crystal_3FBV_ion_ok.prmtop
>
> trajin reeim.xtc
>
>
>
> #analysis with residue at the interface identify by using Chimera (i.e.
> using select > ZONE)
>
> rms first :1-1687.CA
>
> vector A corrplane
> :6,12-14-22,25-30,33-79,83-86,106-137,154-216,222-243,255-258-287-320-322,341-343-366-369,395-466-469,477-534,547-586,596-611-615,628-630-683,684-686-688,700-720-732-735-823,840.CA
>
> vector B corrplane
> :888,896-903-957,966-1005,1016-1018-1031-1034-1036,1047-1050-1103,1104-1106-1108,1120-1140-1143,1144-1150,1152-1243,1260-1261,1265-1273,1279-1281-1289,1293-1295,1299-1346,1350-1353,1373-1375-1404,1422-1484,1489-1510,1522-1559,1554-1587-1589,1607-1610-1616-1633,1634-1636,1662.CA
>
> vectormath vec1 A vec2 B dotangle out angle_tetramer_YEAST_1.dat
>
> run
>
> quit
>
> “
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Received on Wed Mar 25 2020 - 13:00:02 PDT
