[AMBER] using both the ILDN and NMR-based modifications of ff99SB

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Thu, 05 Apr 2012 14:42:38 +0200

Dear Amber users,

We are looking into the possibility of using both the ILDN (from DE
Shaw) and the recent NMR-based modifications (from D.W. Li and R.
Bruschweiler, Angew. Chem. Int. Eng. Ed. 49:6778, 2010) of the ff99SB
force field ...

For the frcmod file, I just combined the frcmod.ff99SBildn and
frcmod.ff99SBnmr by replacing the backbone dihedrals entries in
frcmod.ff99SBildn with those in frcmod.ff99SBnmr

However, I noticed some discrepancies in the distribution of AMBER11
regarding the aminoacid libraries for these 2 modifications ...

The aminoacids libraries for the ILDN modifications are in
"all_amino94ildn.lib" (+ the nt and ct aa). So, I assumed that the file
"all_aminont94.nmr.lib" should contain the corresponding libraries for
the NMR-based modifications ... However, In the leaprc.ff99SBnmr the
original "all_amino94.lib" is loaded, even if "all_amino94.nmr.lib" has
some very tiny differences compared to the original "all_amino94.lib"...
Also the "all_aminont94.nmr.lib" and "all_aminoct94.nmr.lib" do not
exist ...

I also noticed a library file named "all_nucleic94.nmr.lib" ... As far
as I recall the recent NMR-based modifications were done to better fit
the backbone torsion parameters in proteins. Am I missing something ? Or
maybe the file "all_nucleic94.nmr.lib" has nothing to do with the latest
modifications of ff99SB force field and it should get a different name ?

Although I believe that for the NMR-based modifications no change is
required in the libraries we load, I would like to be sure of what we
are doing and ask the following question:
If we load "frcmod.ff99SB-ildn-nmr" (my modified version of frcmod as
explained above) and "all_amino94ildn.lib" (+ nt and ct) are we sure to
use the correct parameters for the NMR-based modifications of ff99SB ?

Thanks for clarifying this,

Best wishes

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Thu Apr 05 2012 - 06:00:03 PDT
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