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

From: Bill Ross <>
Date: Thu, 29 Nov 2018 21:11:57 -0800

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:


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 - 21:30:02 PST
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