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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Received on Mon May 03 2021 - 09:00:02 PDT
