That's a start but there is much more to it. How did you derive the partial
charges for the cyclized part? There will be additional steps after that
too.
On Feb 9, 2016 9:44 AM, "Mohammed Khaled Tumbi" <khaledtumbi.gmail.com>
wrote:
> Dear All:
> I am trying to simulate a large cyclic peptide in complex with protein
> using FF14SB.
> To get cyclic peptide, I made a amide bond between side chains of Asp and
> Lys. (Carboxylic group of Aspartic Acid with Amino group of Lysine).
>
> After that I change atom types for corresponding O,N,C, H to atom types
> similar to peptide bond. (is this correct ?).
>
> But as expected I getting error in leap for missing parameters.
>
> Could not find bond parameter for: C8 - N
> Checking for angle parameters.
> Could not find angle parameter: C - N - C8
> Could not find angle parameter: HP - C8 - N
> Could not find angle parameter: HP - C8 - N
> Could not find angle parameter: C8 - N - H
> Could not find angle parameter: C8 - C8 - N
>
> ** No torsion terms for C-N-C8-C8
> ** No torsion terms for C-N-C8-HP
> ** No torsion terms for C-N-C8-HP
> ** No torsion terms for HP-C8-N-H
> ** No torsion terms for HP-C8-N-H
> ** No torsion terms for C8-C8-N-H
>
> Can any one suggest something.
> Best Regard.
> --
> --------------------------------------------------------
> Tumbi Mohammed Khaled.
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Received on Tue Feb 09 2016 - 07:00:04 PST
