Hi,
There are a couple of issues here.
On Tue, Jul 26, 2022 at 10:33 AM Prathit Chatterjee via AMBER
<amber.ambermd.org> wrote:
> CPPTRAJ: Trajectory Analysis. V4.25.6
Please upgrade to a more recent version of cpptraj (from AmberTools 22
or from the GitHub site: https://github.com/Amber-MD/cpptraj). That
will get rid of the CMAP etc warnings.
>
> Error: PDB step5_prot.4_frame2.pdb: No frames read. atom=8418 expected
> 1394424.
Your topology and input trajectory have different #s of atoms. Based
on the file naming I'm guessing that step5_prot.4_frame2.pdb only has
the protein, while step3_input.parm7 has the entire system (solvent
etc). If the protein is all you want you can just use the PDB as your
topology:
cpptraj -p step5_prot.4_frame2.pdb -y step5_prot.4_frame2.pdb -x
step5_prot.4_frame2.rst7
Note also that cpptraj can use PSF files directly as topology files.
-Dan
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Received on Mon Aug 08 2022 - 07:30:03 PDT
