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 - 07:30:03 PST
