On Tue, Sep 15, 2015, Jonathan Gough wrote:
>
> Thy cyclic peptide has an un-natural bond. An Internal LYS.NZ--ASP.CG amide
> bond.
>
> leap (as far as I can tell) made the bond. However, ff14SB doesn't have the
> requisite bond/angle/torsion parameters for the non-native LYS-ASP amide
> bond. (hence why I was asking about needing to make a new residue). At the
> most basic level it's just an aliphatic amide bond, is there a way to
> import these from gaff yet retaining the rest of the ff14SB parameters?
Here's one approach: save your peptide as a mol2 or off file; then use
a text editor to change the atom types around the LYS-ASP connection to
the standard H,N,C,O types that Amber would use for ordinary amide bonds.
When you load this back in to LEaP, all the needed parameters should be
present.
[If you use xleap, select the atoms around the LYS-ASP region, and choose
"Edit selected atoms": that will bring up a spreadsheet-like widget where
you can edit the atom types.]
...good luck...dac
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Received on Tue Sep 15 2015 - 15:00:04 PDT
