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:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
> 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$n-ATMREORDR = ON/OFF)
(the atom types are listed in that file and can be reused in a new job
and provided in the Project.config input file)
torsion terms are mandatory while improper torsion terms are not
> I am using ff99SB. There were some bonds, angles and dihedrals
> missing when parameterizing, but I have used the analogous
> parameters from the gaff force field, and received an frcmod file
> which I have uploaded, and amber is not complaining about any other
> of those parameters. (One of these that I have in the frcmod file is
> CT-NT-P-OS). I have attached the frcmod.known file that I have used.
using the Re_Fit mode you can re-fit the charges, redefine the FF atom
types, add lon pairs, etc... based on the QM computation carried out
in the previous job...
See again
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
then when all is check and supposed ok; see:
http://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#6
tar -jxvf P$x.tar.bz2
cd P$x/Data-R.E.D.Server/Data-Default-Proj
xleap -f leaprc.q4mdfft
regards, Francois
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Sat Aug 20 2016 - 02:00:02 PDT
