unanswered Cis peptide bond problem with backward mapping

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4 months 2 weeks ago #7700 by maxime.louet
maxime.louet created the topic: Cis peptide bond problem with backward mapping
Hello everyone,

I'm trying to backmap a protein from CG to all-atom. My problem is: I observed quite often (about 2%) of the amino-acids being backmapped with cis peptide bonds (and more especially proline). I know cis/trans isomerizations happen in nature but not at this high rate (as far I know it's far less than 1%). I tried to add dihedral restraints to the all-atom itp file to maintain the omega angles at 180° with no luck. My guess is that this could be due to the position restraints which should be higher in magnitude. When I increase the force for the dihedral restraints the system explodes during the MD phase. I could remove these position restrains but I'd rather prefer to keep them as much as possible. Any idea why there is so much cis isomers of the peptide bond? Is that a common problem for backward mapping in all-atom? or a specific to some proteins? I note that the starting structure (I mean at the very beginning, before mapping to coarse grain and simulations), all peptide bonds were in trans conformation. I'm using the charmm36 force field for the backmapping routine. I would like to note as well that this cis-isomerization could affect different residues for different backmapping runs from the same CG conformation and seems to be quite random, the residue being trans for 1 run and cis for another run.

Any idea would be very much appreciated.

Maxime

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