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

From: FyD <>
Date: Sat, 20 Aug 2016 10:55:11 +0200

Dear Cecilia,

The frcmod.unknown file list the unknown FF parameters; the later can
be provided using the frcmod.user input file in a second job (Re_Fit
mode); please see:

> 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 would check the FF atom types generated by PyRED: they can be
slightly adapted in a second job (Re_Fit mode) using the
MOLECULE$n-ATMTYPE keyword ($n: molecule id)
See the output file
Data-R.E.D.Server/Data-Default-Proj/Project-out.config (for the new
atom order: the input atom order is different from the output atom
order by default; see MOLECULE$n-ATMREORDR = ON/OFF)
(the atom types are listed in that file and can be reused in a new job
and provided in the Project.config input file)

torsion terms are mandatory while improper torsion terms are not

> 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.

using the Re_Fit mode you can re-fit the charges, redefine the FF atom
types, add lon pairs, etc... based on the QM computation carried out
in the previous job...
See again

then when all is check and supposed ok; see:
   tar -jxvf P$x.tar.bz2
   cd P$x/Data-R.E.D.Server/Data-Default-Proj
   xleap -f leaprc.q4mdfft

regards, Francois

           F.-Y. Dupradeau

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Received on Sat Aug 20 2016 - 02:00:02 PDT
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