Hi,
It's not clear to me what's going wrong. It looks like the run doesn't
actually start based on your second screenshot. The amber16 version of
cpptraj is pretty old at this point. I'd try to use a more up to date
version. Also, debugging will be easier if you first try to analyze a
smaller number of frames (like 10) first.
-Dan
On Tue, Apr 21, 2020 at 5:48 AM Prathit Chatterjee
<prathit.biophysics.gmail.com> wrote:
>
> Dear Experts in AMBER Community,
>
> I am relatively new to extensively using AMBER.
> I am trying to figure out pairwise interaction by using cpptraj, following
> AMBER16..
>
> But, an error is coming which I cannot resolve:
>
> In the cpptraj input file, it is written as follows (*THE LINE FOR
> ACTUAL CALCULATION HIGHLIGHTED*):
>
> [image: image.png]
> Also, copying the line of command provided in the fileaj (*highlighted in
> blue*):
> pairwise EVDW noelec :1-43.C,CA,N,O :1-43AC,CA,N,O cutvdw 5.4 cutevdw 1.0
> out All.pairwise.dat eout eout.pairwise.dat vmapout vmap.dat avgout avg.dat
>
> But, the out.log is showing error as follows (*ALSO HIGHLIGHTED*):
>
> [image: image.png]
> Also the error message is provided below (*highlighted in blue*):
> [pairwise EVDW noelec :1-43.C,CA,N,O :1-43AC,CA,N,O cutvdw 5.4 cutevdw 1.0
> out All.pairwise.dat eout eout.pairwise.dat vmapout vmap.dat avgout avg.dat]
> PAIRWISE: Atoms in mask [:1-43.C,CA,N,O].
> Energy info for each atom will be written to eout.pairwise.dat
> Average energies will be written to 'avg.dat'
> Only average energy components that satisfy the cutoffs will be
> printed.
> Eelec print absolute cutoff (kcal/mol): 1.0000
> Evdw print absolute cutoff (kcal/mol) : 1.0000
> VDW energy matrix set: EVDW[VMAP]
> VDW energy matrix written to 'vmap.dat'
> Elec. energy matrix set: EVDW[EMAP]
> Warning: Set 'EVDW[EVDW]' contains no data.
> Warning: Set 'EVDW[EELEC]' contains no data.
> Warning: File 'All.pairwise.dat' has no sets containing data.
> Warning: Set 'EVDW[VMAP]' contains no data.
> Warning: File 'vmap.dat' has no sets containing data.
> TIME: Total execution time: 0.6524 seconds.
>
> Kindly please help me/provide me with some guidelines in solving this minor
> issue...
> Sincerely awaiting your kind response,
>
> Thanking you,
> Regards,
> Prathit Chatterjee
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Received on Wed Jun 24 2020 - 09:30:04 PDT
