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

From: David A Case <>
Date: Fri, 30 Nov 2018 08:06:06 -0500

On Fri, Nov 30, 2018, Pietro Aronica wrote:

>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.

Bill is correct: the only easy way to handle cyclic systems is to modify
the addPdbResMap commands. And, if you have both a terminal GLY and a
non-terminal GLY in the same system, you could have a problem. In that
case, however, you could change what you consider to be the "start" and
the "end of the cyclic system to avoid the name clash. I agree that
this is rather inelegant.

[Partial explanation: back in prehistory, a decision was made to
internally call terminal residues things like NGLY and CGLY. This
avoids name collisions with the rest of the PDB, but 4-letter residue
codes cannot be entered into a PDB format, so the easier alternative of
just editing the input PDB file to indicate which variant you want is
not available.

Further rant: the PDB standard, even for mmcif, is very deficient in
allowing the specification of different protonation or tautomer states
of a "parent" residue. Basically, user's codes are expected to examine the
structure (e.g. presence and location of hydrogens) to figure out what
is really going on. The pdb4amber code does this for "HIS", and
could/shoud be extended to handle other common ambigous residue names.
But the output of pdb4amber is another PDB file, so cannot make use of
4-letter residue names.]


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Received on Fri Nov 30 2018 - 05:30:03 PST
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