Dear all,
This is more trivial questions but I am getting error message while
calculating distance between two atoms using cpptraj.
Basically I want to calculate the distance between acceptor atom 3981 and
donor atom 3092 for all frames during the simulation and I would like to
calculate the average and standard deviation from the output for this
particular hydrogen bond in excel.
#Acceptor DonorH Donor Frames
Frac AvgDist AvgAng
PRO_245.O_3981 TYR_189.HH_3093 TYR_189.OH_3092 8984
0.9982 2.7331 163.7062
I tried following based on the previous suggestions in mailing list:
distance DIST1 .3981.3092 out dist1.out
But I got error message that says ; Error: distance requires 2 masks
I also tried :
distance DIST :3981.O :3092.OH
And I got no output with the following message :
parm x.prmtop
Reading 'x.prmtop' as Amber Topology
> trajin Prod.mdcrd
Reading 'Prod.mdcrd' as Amber NetCDF
> distance DIST :3981.O :3092.OH
DISTANCE: :3981.O to :3092.OH, center of mass.
> run
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: x.prmtop, 55934 atoms, 17450 res, box: Orthogonal, 17179 mol, 17171
solvent
INPUT TRAJECTORIES (1 total):
0: 'Prod.mdcrd' is a NetCDF AMBER trajectory, Parm x.prmtop (Orthogonal
box) (reading 9000 of 9000)
Coordinate processing will occur on 9000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'x.prmtop' (1 actions):
0: [distance DIST :3981.O :3092.OH]
:3981.O (0 atoms) to :3092.OH (0 atoms)
Warning: One or both masks have no atoms.
Warning: Setup incomplete for [distance]: Skipping
----- Prod.mdcrd (1-9000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 9000 frames and processed 9000 frames.
TIME: Avg. throughput= 203.0209 frames / second.
ACTION OUTPUT:
DATASETS (1 total):
DIST "DIST" (double, distance), size is 0
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 44.3304 s (100.00%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0000 s ( 0.00%)
TIME: Run Total 44.3305 s
---------- RUN END ---------------------------------------------------
> quit
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Any inputs would be greatly appreciated.
Jag S
Michigan State U
Chemistry
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Received on Fri Aug 11 2017 - 10:00:03 PDT
