NMR Refinement of DNA and RNA Duplexes | Structure refinement in AMBER

add that line ,

i'm going to use tleap here

leap automatically add missing H s

if you want to understand this paramtop format follow me..
i'm just showing where is this .. :)

i have no idea how to fix le me think
no idea how to fix .. so , lets look into theories coz we have files ..

$iat[3]=0 which mean distance

$IAT(4) = 0, this is an angle restraint.

iat= 10, 27, 35 , , we only define 3 vavlues ... which is angle

a plane-point angle restraint, i dont know what these are..

between r1 and r4 it is harmonic way .. i mean a curve ,

left to r1 is linear , so do the right to R4 is linear .. . between r1 and r2 is curve... also r3 to r4 is curve ... between r2 - r3 is i need to investigate .. :)

Torsion angle restraints
this is what i'm interested in :))))))))))

did you notice that location also different? what mention in the tutorial ...
it is old, but anyway ... moving forward..

im not going for Watson crick coz it is another distance as well confusing. but lets have a look iat has only 2 variables mean distance

okay wotson restrains also important coz the two strands may separate during the high-temperature regime and not be able to renature to the correct conformation upon cooling.

not going to run minimizations

this nmropt=1, is important coz .. let me show , nmropt=1, when 1 amber looking for a restrain file RST file ..

go to suppose folder and
sudo bash ./Makefile

/home/hutch/amber18/AmberTools/examples/suppose/suppose

/home/hutch/amber18/AmberTools/examples/suppose/suppose (-mat) (-rot0 (-mean) -sd -cmp pdbfile
-pr atom_sel -fit atom_expr -calc atom_expr pdbfiles

ls

how to get output from cordinate files ?

-x file are cannot be read they are binary ...
but in tutorial is it soemthing else
it may be both types binary and normal .. i'm not sure ..
lets go forward

restart files can be binary / or normal ?? however lets go..

pdbs are lot different

trajectories also can be normal file not binary :))))))))))

thats all guys good luck ! :))