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

From: Yu Chen via AMBER <amber.ambermd.org>
Date: Fri, 10 Nov 2023 19:23:02 +0100

Dear Amber Community,

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 > tleap.combine.in <<EOF
                rcp = loadpdb ${rcp_nm}amber_f.pdb
                nmLig = loadpdb rename${nmLigFile}.pdb
                comp = combine{rcp nmLig}
                savepdb comp comp.pdb
                tleap -s -f tleap.combine.in > tleap.combine.out

I would greatly appreciate any insights or guidance on how to address this issue and successfully combine the protein and ligand structures without introducing 'TER' between each residue.

Best regards,
Yu Chen
Yu Chen (M.Sc., Frau/Ms)
Ph.D Student
Freie Universität Berlin
Department of Biology, Chemisty, and Pharmacy
Institute of Pharmacy
Research Group Prof. Dr. Gerhard Wolber
Königin-Luise-Str. 2+4 , 14195
Room 180, Front Building
Berlin / Germany

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