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

From: David Case via AMBER <>
Date: Sat, 11 Nov 2023 16:05:44 -0700

On Sat, Nov 11, 2023 at 11:24 AM Yu Chen <> wrote:

> `
> 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 looks like you are not loading any leaprc files (for proteins and water,
say). Are you not seeing tons of messages like this one:

     Creating new UNIT for residue: GLY sequence: 303 ?

This means that tleap doesn't know about connectivity between residues
(since that information is stored in the libraries you failed to load.)
Since there is no bonding information available, tleap inserts TER cards
between residues.

You need to study carefully what happens at each "loadpdb" step, and fix
the problems.

FWIW: this has nothing to do with the combine command: you would get
similar behavior just typing "savepdb rcp rcp.pdf" above.

Finally, if you have components from a few separated PDB files that all
need to be included in your final system, I still recommend using a text
editor to create the "comp.pdb" file. Then use a single loadpdb command in
tleap. At this stage, look at any warnings and errors that tleap produces.

...good luck...dac
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Received on Sat Nov 11 2023 - 15:30:03 PST
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