Re: [AMBER] Creating rst7 file with CHARMM-GUI generated parm7 and pdb files (Charmm36 force field)

From: Daniel Roe via AMBER <amber.ambermd.org>
Date: Mon, 8 Aug 2022 10:15:08 -0400

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
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