[AMBER] MD simulation with non natural amino acid, parameterized using the RED server

From: Cecilia Lindgren <cecilia.lindgren.umu.se>
Date: Wed, 17 Aug 2016 12:56:24 +0000

Dear Amber users,

I want to run MD simulations of a protein with one non-natural amino acid. I have used the RED server to parameterize this amino acid (P5327), and it seems fine. However, when I use tleap to build the inpcrd and prmtop files I get the following error message:

Building proper torsion parameters.
** No torsion terms for CT-NT-P-OS
** No torsion terms for CT-NT-P-OS
** No torsion terms for OS-P-NT-CT
** No torsion terms for OS-P-NT-CT

I am using ff99SB. There were some bonds, angles and dihedrals missing when parameterizing, but I have used the analogous parameters from the gaff force field, and received an frcmod file which I have uploaded, and amber is not complaining about any other of those parameters. (One of these that I have in the frcmod file is CT-NT-P-OS). I have attached the frcmod.known file that I have used.

Does anyone have any suggestions on what I can try?

Best regards,
Cecilia


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Received on Wed Aug 17 2016 - 06:00:04 PDT
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