Re: [AMBER] Formation of a cyclic peptide

From: Bill Ross <>
Date: Sat, 19 Sep 2020 02:09:00 -0700

If you are expecting a bond to show when loading the pdb, unless it has
CONECT records/lines in it, no software package can 'see' a nonstandard

If your residue types switched to nonterminal ones, that's another matter.

In any case, copy/pasting any errors or warnings you see in leap.log
will help dig deeper.


On 9/19/20 12:58 AM, RIMJHIM MORAL wrote:
> Dear all,
> 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.
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Received on Sat Sep 19 2020 - 02:30:02 PDT
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