Re: [AMBER] Formation of a cyclic peptide

From: Dr. Anselm Horn <>
Date: Tue, 22 Sep 2020 10:05:59 +0200


I guess, your problem is the automatic transformation of the terminal
residues into their ionic forms via leap, i.e. protonated N-terminus and
deprotonated C-terminus. This is done in leap regardless of any bond
command you issue.

A simple solution for cyclic peptides is to provide leap with the actual
sequence of your system, i.e. using the command loadpdbusingseq.
Assuming a sample peptide with eight residues (AGLVDNKC), you could
issue something like the following in your leap input:

# [... initial parameter loading]
# Define sequence for cyclic peptide without terminal NALA and CCYS
# Load structure of cyclic peptide
cyclicpeptide = loadPDBusingseq peptide.pdb seq
# Form cyclic peptide bond
bond cyclicpeptide.1.N cyclicpeptide.8.C
# [ ... other leap stuff, save files etc]

Other ways to alleviate the automatic terminal residue transformation
exist, though (see the Amber mailing list archive for similar questions).

I hope this helps.



Bill, sorry for extra-posting!

On 09/19/2020 11:09 AM, Bill Ross wrote:
> 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
> bond.
> 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.
> Bill
> 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.
>> _______________________________________________
>> AMBER mailing list

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Received on Tue Sep 22 2020 - 01:30:03 PDT
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