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

From: Pietro Aronica <>
Date: Fri, 30 Nov 2018 13:37:21 +0800

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"


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 Thu Nov 29 2018 - 22:00:02 PST
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