> Warning: One or both masks have no atoms.
> :3981.O (0 atoms) to :3092.OH (0 atoms)
try :3981.O and :3092.OH
Hai
On Fri, Aug 11, 2017 at 12:42 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 11 2017 - 10:00:03 PDT
