Re: [AMBER] Command 'combine' in 'tleap' Introducing 'TER' Between Residues

From: David A Case via AMBER <>
Date: Sat, 11 Nov 2023 10:52:07 -0700

On Fri, Nov 10, 2023, Yu Chen via AMBER wrote:
>I hope this message finds you well. I am currently using Ambertools 22.0,
>installed via conda, and am encountering an issue while attempting to
>combine a protein (or RNA) and ligand PDB file using the `combine` method
>in tleap. My ultimate goal is to generate `prmtop` and `inpcrd` files for
>subsequent simulations.
>Upon inspecting the combined PDB file in a text editor, I observed that
>each residue, whether belonging to the protein or RNA, is separated by
>'TER', resulting in the entire system being fragmented.
>Here's a snippet of the code from my bash script:
> `
> cat > <<EOF
> rcp = loadpdb ${rcp_nm}amber_f.pdb
> nmLig = loadpdb rename${nmLigFile}.pdb
> comp = combine{rcp nmLig}
> savepdb comp comp.pdb
> quit
> tleap -s -f > tleap.combine.out
> `
It's hard to say what went wrong, without seeing the input pdb files you
used. But I'd recommend using a text editor (not the tleap "combine"
command) to create the "comp.pdb" file.

[Are you sure the problem is related to the combine command? It seems more
likely that something is amiss with the ${rcp_nm}amber_f.pdb file.]


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Received on Sat Nov 11 2023 - 10:00:02 PST
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