Re: [AMBER] Head-to-tail cyclized Peptides

From: Dr. Anselm Horn <>
Date: Fri, 30 Nov 2018 16:16:27 +0100

Dear all,

another, less invasive way to create cyclized peptides might be to use
the leap command loadPDBusingSeq, where you explicitely provide the
sequence as a list; in this list you must specify any terminal residue,
e.g. NGLY or CTYR (cf leap manual). Thus, by omitting the terminal
residue names for the initial and the last residue, but instead just
using the normal mid-chain names, and afterwards manually adding a bond
between the N of the first and C of the last residue, a cyclization
should be possible.

# Leap input
seq = {

a = loadPDBusingseq gly6.pdb seq

# Cyclize peptide
bond a.1.N a.6.C

The only drawback is that you have to write an explicit sequence of your
complete peptide system.

Best regards


On 11/30/2018 06:37 AM, Pietro Aronica wrote:
> Yeah, the suggestion in that email is precisely what I am doing, getting
> rid of the mapping. It's good to know that people have been having the
> same issue for five years! I guess there really isn't a more "official"
> solution.
> Pietro
> On 30/11/2018 13:11, Bill Ross wrote:
>> There was a cyclic molecule demo, crown ether.. I beat the *** out of it
>> once upon a time, but looks like it was retired. :-) It seems there
>> should be one cyclic demo, and what better molecule could one choose?
>> Here's something that may still work:
>> Bill
>> On 11/29/18 8:46 PM, Pietro Aronica wrote:
>>> Hello all,
>>> I have several peptides where the N-terminus is linked in a peptide bond
>>> to the C-terminus of the same peptide. I have a conect record in the pdb
>>> file or bond command in the leap input file to link those two atoms.
>>> My issue is that when the peptide is loaded into leap, it sees the two
>>> residues and assumes that they are terminal, and thus adds H1, H2 and H3
>>> at one end and OXT at the other. This is of course unnecessary and not
>>> representative of my peptides. A quick workaround I have used is to to
>>> comment out the terminal mapping in the cmd file for the relevant amino
>>> acids; if leap doesn't know that a terminal GLY is supposed to be
>>> replaced by NGLY, it won't add the extra atoms and assign the correct
>>> charges when creating the prmtop.
>>> This solution works for now but it is inelegant and might run into
>>> issues later if there is another amino acid of the same kind in my
>>> system that is terminal which would thus not be mapped. I have looked
>>> through leap's commands and syntax but not found anything. Does anyone
>>> know of a better way to tell leap that a peptide is head-to-tail cyclised?
>>> Thanks in advance
>>> Pietro
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Received on Fri Nov 30 2018 - 07:30:02 PST
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