Hi,
On Fri, May 7, 2021 at 5:37 AM Richard Kullmann
<Richard.Kullmann.mpikg.mpg.de> wrote:
> It does not seem to give any warnings about corrupted trajectory, but it
> states that 0 native contacts were set up...May this be the reason for
> all the "-nan" entries?
Yeah, that's it. The fact that there are no contacts leads to a divide
by zero error. I'll fix it on GitHub.
-Dan
>
> Thank you and best regards,
>
> Richard
>
>
> CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.13)
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 05/07/21 11:26:41
> | Available memory: 116.255 GB
>
> INPUT: Reading input from 'contact.1.1904.cpptraj'
> [parm ../../remd/cpptrajfiles/topology-no_water.parm7]
> Reading '../../remd/cpptrajfiles/topology-no_water.parm7' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> [trajin remd_combine.1904.1.nc]
> Reading 'remd_combine.1904.1.nc' as Amber NetCDF
> [nativecontacts :1-500&!.H= :501-503&!.H= distance 4.5 contactpdb
> tri_1904.1.pdb]
> Warning: No reference structure specified. Defaulting to first.
> NATIVECONTACTS: Mask1=':1-500&!.H*' Mask2=':501-503&!.H*', native
> contacts set up based on first frame.
> Distance cutoff is 4.5 Angstroms, imaging is on.
> Mask selection will not include solvent.
> Data set name: Contacts_00001
> Contact stats will be written to 'STDOUT'
> Contact res pairs will be written to 'STDOUT'
> Contact PDB will be written to 'tri_1904.1.pdb'
> [run]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: topology-no_water.parm7, 8058 atoms, 514 res, box: Trunc. Oct., 13 mol
>
> INPUT TRAJECTORIES (1 total):
> 0: 'remd_combine.1904.1.nc' is a NetCDF AMBER trajectory with
> coordinates, time, replicaDims, replica indices, coordinate indices,
> box, 1 replica dimensions, Parm topology-no_water.parm7 (Trunc. Oct.
> box) (reading 12933 of 12933)
> Coordinate processing will occur on 12933 frames.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'topology-no_water.parm7' (1 actions):
> 0: [nativecontacts :1-500&!.H= :501-503&!.H= distance 4.5 contactpdb
> tri_1904.1.pdb]
> Mask [:1-500&!.H*] corresponds to 4063 atoms.
> Mask [:501-503&!.H*] corresponds to 33 atoms.
> 4063 potential contact sites for ':1-500&!.H*'
> 33 potential contact sites for ':501-503&!.H*'
> Imaging enabled.
> ----- remd_combine.1904.1.nc (1-12933, 1) -----
> Using first frame to determine native contacts.
> Mask [:1-500&!.H*] corresponds to 4063 atoms.
> Mask [:501-503&!.H*] corresponds to 33 atoms.
> Setup 0 native contacts:
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 12933 frames and processed 12933 frames.
> TIME: Avg. throughput= 53.4853 frames / second.
>
> ACTION OUTPUT:
> CONTACTS: Contacts_00001
> Writing contacts PDB to 'tri_1904.1.pdb'
> TIME: Analyses took 0.0000 seconds.
>
> DATASETS (2 total):
> Contacts_00001[native] "Contacts_00001[native]" (integer), size is
> 12933 (51.732 kB)
> Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size
> is 12933 (51.732 kB)
> Total data set memory usage is at least 103.464 kB
>
> DATAFILES (3 total):
> STDOUT (Native Contacts)
> tri_1904.1.pdb (Contact PDB)
> STDOUT (Contact Res Pairs)
>
> RUN TIMING:
> TIME: Init : 0.0001 s ( 0.00%)
> TIME: Trajectory Process : 241.8046 s ( 99.98%)
> TIME: Action Post : 0.0371 s ( 0.02%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0001 s ( 0.00%)
> TIME: Other : 0.0001 s ( 0.00%)
> TIME: Run Total 241.8419 s
> ---------- RUN END ---------------------------------------------------
>
>
> On 5/3/21 5:48 PM, Daniel Roe wrote:
> > Hi,
> >
> > What version of cpptraj are you using? Are there any warnings in the output
> > about possible corruption in the trajectory?
> >
> > -Dan
> >
> > On Mon, May 3, 2021 at 10:28 AM Richard Kullmann <
> > Richard.Kullmann.mpikg.mpg.de> wrote:
> >
> >> Hi all,
> >>
> >> I am trying to determine the average number of contacts over a
> >> trajectory between receptor (residue 1 to 500) and ligand (residue 501
> >> to 503) and create a pdb with corresponding beta-factor. The script I
> >> use is the following:
> >>
> >> parm ../../remd/cpptrajfiles/topology-no_water.parm7
> >> trajin remd_combine.1904.1.nc
> >> nativecontacts :1-500&!.H= :501-503&!.H= distance 4.5 contactpdb
> >> tri_1904.1.pdb
> >> run
> >> quit
> >>
> >> This runs through, but in the end, all beta factors are just -nan.
> >> What am I doing wrong or is what I am trying to do just not possible?
> >>
> >> Thanks a lot in advance for your help.
> >>
> >> Best regards,
> >>
> >> Richard
> >>
> >> _______________________________________________
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> >>
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Received on Tue May 11 2021 - 12:30:02 PDT
