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

From: David A Case <>
Date: Wed, 17 Aug 2016 10:13:46 -0400

On Wed, Aug 17, 2016, Cecilia Lindgren wrote:
> 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.

Can you list the exact commands you gave to tleap? Have you carefully examined
the leap.log file to see there are any messages relating the
"loadAmberParams frcmod.known" command?


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Received on Wed Aug 17 2016 - 07:30:02 PDT
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