Dear Experts,
Greetings!
I am trying to calculate the RMSF of C-alpha atoms by residues of my dimer
systems of interest.
The one of the code format is as follows:
parm ../../../init_0.15IC.parm7
reference ../../../step7_5.rst7 [EqRef]
trajin ../../smd.12.1_equil.nc 1 50
#centering
strip :WAT
strip :K+
strip :Cl-
center .1-5142 mass origin
image origin center familiar
#RMSD
# CA RMSD to the reference structure 2 (excluding the terminal residues)
rmsd ref [EqRef] .1-5142.CA out RMSD_CA_dimer_12.dat
rmsd ref [EqRef] .1-2571.CA out RMSD_CA_proA_12.dat
# Rg
radgyr out Rg_proA_12.dat .1-2571
*# CA RMSF vs. residue*
*atomicfluct out RMSF_CA_proA_12.dat .1-2571.CA byres*
In the above, .1-2571 is the index number of the atoms of one of my
monomers.
This is because my pdb generated with charmmgui, for charmm36 force field
is as follows (showing the part where the coordinates of one monomer end
and the other begin):
..................
ATOM 2558 HB2 LEU 162 21.845 -12.084 -12.450 1.00 0.00 PROA
H
ATOM 2559 CG LEU 162 21.543 -10.006 -12.003 1.00 0.00 PROA
C
ATOM 2560 HG LEU 162 22.000 -10.025 -10.985 1.00 0.00 PROA
H
ATOM 2561 CD1 LEU 162 22.625 -9.623 -13.002 1.00 0.00 PROA
C
ATOM 2562 HD11 LEU 162 22.218 -9.615 -14.035 1.00 0.00 PROA
H
ATOM 2563 HD12 LEU 162 23.465 -10.353 -12.961 1.00 0.00 PROA
H
ATOM 2564 HD13 LEU 162 23.019 -8.611 -12.767 1.00 0.00 PROA
H
ATOM 2565 CD2 LEU 162 20.426 -8.975 -12.008 1.00 0.00 PROA
C
ATOM 2566 HD21 LEU 162 19.581 -9.321 -11.380 1.00 0.00 PROA
H
ATOM 2567 HD22 LEU 162 20.055 -8.816 -13.042 1.00 0.00 PROA
H
ATOM 2568 HD23 LEU 162 20.802 -8.006 -11.614 1.00 0.00 PROA
H
ATOM 2569 C LEU 162 19.448 -13.305 -11.823 1.00 0.00 PROA
C
ATOM 2570 OT1 LEU 162 19.639 -14.379 -11.192 1.00 0.00 PROA
O
ATOM 2571 OT2 LEU 162 18.774 -13.222 -12.884 1.00 0.00 PROA
O
TER
ATOM 2572 N LEU 1 1.215 -2.124 14.492 1.00 0.00 PROB
N
ATOM 2573 HT1 LEU 1 1.619 -1.263 14.916 1.00 0.00 PROB
H
ATOM 2574 HT2 LEU 1 1.334 -2.951 15.122 1.00 0.00 PROB
H
ATOM 2575 HT3 LEU 1 0.198 -2.022 14.307 1.00 0.00 PROB
H
ATOM 2576 CA LEU 1 1.904 -2.366 13.233 1.00 0.00 PROB
C
ATOM 2577 HA LEU 1 2.956 -2.507 13.444 1.00 0.00 PROB
H
ATOM 2578 CB LEU 1 1.330 -3.606 12.541 1.00 0.00 PROB
C
ATOM 2579 HB1 LEU 1 1.875 -3.779 11.584 1.00 0.00 PROB
H
ATOM 2580 HB2 LEU 1 0.263 -3.424 12.263 1.00 0.00 PROB
H
ATOM 2581 CG LEU 1 1.373 -4.910 13.344 1.00 0.00 PROB
C
ATOM 2582 HG LEU 1 0.931 -4.777 14.343 1.00 0.00 PROB
H
ATOM 2583 CD1 LEU 1 0.654 -6.021 12.596 1.00 0.00 PROB
C
ATOM 2584 HD11 LEU 1 1.131 -6.199 11.611 1.00 0.00 PROB
H
ATOM 2585 HD12 LEU 1 -0.411 -5.750 12.419 1.00 0.00 PROB
H
ATOM 2586 HD13 LEU 1 0.692 -6.968 13.176 1.00 0.00 PROB
H
ATOM 2587 CD2 LEU 1 2.808 -5.309 13.651 1.00 0.00 PROB
C
ATOM 2588 HD21 LEU 1 3.264 -4.620 14.392 1.00 0.00 PROB
H
..................
However, my results for rmsf provide me the results for all the residues
(including both the monomers), instead of only one of the monomers.
Please let me know how I can resolve this issue.
Regards,
Prathit Chatterjee
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Received on Sun Feb 05 2023 - 22:00:02 PST
