Re: [AMBER] Formation of a cyclic peptide

From: David A Case <>
Date: Sat, 19 Sep 2020 08:17:46 -0400

On Sat, Sep 19, 2020, RIMJHIM MORAL wrote:
> I am trying to generate a pdb of a cyclic peptide. I am using
> the command "bond m.1.N m.8.C" (m is the defined name of the
> pdb in xleap) to form the bond between the terminal residues
> but after saving the pdb, it is automatically being converted
> into the free terminals. Please suggest me if there is any
> other way to do the same. Thank you in advance.

Add a "clearPdbResMap" command after loading all of your leaprc files;
this should remove the conversion of terminal residues, which would
otherwise be the default. Then load your pdb file, and issue the bond
command described above.

...good luck....dac

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Received on Sat Sep 19 2020 - 05:30:02 PDT
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