Re: [AMBER] Residue mutation and side chains

From: Carlos Simmerling <>
Date: Wed, 12 Sep 2018 12:25:16 -0400

Leap can build them, but it doesn't have a good way to optimize their
rotamers prior to MD.
I suggest using tools made for this purpose, like those in swissPDBviewer,
or the SCWRL program. There are probably others too, and it depends on
whether your mutations are solvent exposed (fairly easy) or buried (harder).

On Wed, Sep 12, 2018 at 7:02 AM Benjamin Clausen <>

> Hello
> I am trying to carry out a residue mutation in AMBER. As far as I have
> understood I can use "pdb4amber" to mutate residues, but the resulting
> mutations only leave the backbone in the pdb file. Is there any way I can
> make AMBER put in the missing side chain of the mutated residues?
> The input I have used for mutation is:
> pdb4amber -i in.pdb -o out.pdb -m "94-GLY,94-ASP,217-GLU,217-GLN"
> Best regards Benjamin
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Received on Wed Sep 12 2018 - 09:30:02 PDT
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