[AMBER] Head-to-tail cyclized Peptides

From: Pietro Aronica <pietroa.bii.a-star.edu.sg>
Date: Fri, 30 Nov 2018 12:46:30 +0800

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

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Received on Thu Nov 29 2018 - 21:00:03 PST
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