AMBER ff99SB-ILDN-NMR in amber format A hybrid set of force field files for AMBER, that combines the side chain mods of ff99sbildn (Lindorff-Larsen 2010) and ff99SB-nmr1 (Li and Bruschweiler 2010).
Prepared by: Vincent Voelz
The entire ff99sb-nmr1 modification is just these parameters:
From D.W. Li and R. Bruschweiler, Angew. Chem. Int. Eng. Ed. 49:6778, 2010
MASS
BOND
ANGL
DIHEDRAL
C -N -CT-C 1 0.41 0.0 -4. four amplitudes and
C -N -CT-C 1 0.52 0.0 -3. phases for phi
C -N -CT-C 1 0.11 0.0 -2.
C -N -CT-C 1 0.00 0.0 1.
N -CT-C -N 1 0.13 0.0 -4. four amplitudes and
N -CT-C -N 1 0.75 180.0 -3. phases for psi
N -CT-C -N 1 1.21 180.0 -2.
N -CT-C -N 1 0.64 180.0 1.
CT-CT-N -C 1 0.32 0.0 -4. four amplitudes and
CT-CT-N -C 1 0.13 0.0 -3. phases for phi'
CT-CT-N -C 1 1.63 0.0 -2.
CT-CT-N -C 1 2.43 0.0 1.
CT-CT-C -N 1 0.25 0.0 -4. four amplitudes and
CT-CT-C -N 1 0.70 0.0 -3. phases for psi'
CT-CT-C -N 1 0.31 0.0 -2.
CT-CT-C -N 1 0.41 180.0 1.
NONB
All you need to do is to find the corresponding lines in the ff99SB-ildn frcmod file and replace them with them ff99sb-nmr1 parameters:
cmd/ lib/ parm/
vvs-MacBook-Pro:amberff99sb-ildn-nmr vv$ cat ff99SB-ildn/dat/leap/parm/frcmod.ff99SBildn | grep "C -N -CT-C"
C -N -CT-C 1 0.00 0.0 -4. four amplitudes and
C -N -CT-C 1 0.42 0.0 -3. phases for phi
C -N -CT-C 1 0.27 0.0 -2.
C -N -CT-C 1 0.00 0.0 1.
vvs-MacBook-Pro:amberff99sb-ildn-nmr vv$ cat ff99SB-ildn/dat/leap/parm/frcmod.ff99SBildn | grep "N -CT-C -N"
N -CT-C -N 1 0.00 0.0 -4. four amplitudes and
N -CT-C -N 1 0.55 180.0 -3. phases for psi
N -CT-C -N 1 1.58 180.0 -2.
N -CT-C -N 1 0.45 180.0 1.
vvs-MacBook-Pro:amberff99sb-ildn-nmr vv$ cat ff99SB-ildn/dat/leap/parm/frcmod.ff99SBildn | grep "CT-CT-N -C"
CT-CT-N -C 1 0.00 0.0 -4. four amplitudes and
CT-CT-N -C 1 0.40 0.0 -3. phases for phi'
CT-CT-N -C 1 2.00 0.0 -2.
CT-CT-N -C 1 2.00 0.0 1.
vvs-MacBook-Pro:amberff99sb-ildn-nmr vv$ cat ff99SB-ildn/dat/leap/parm/frcmod.ff99SBildn | grep "CT-CT-C -N"
CT-CT-C -N 1 0.00 0.0 -4. four amplitudes and
CT-CT-C -N 1 0.40 0.0 -3. phases for psi'
CT-CT-C -N 1 0.20 0.0 -2.
CT-CT-C -N 1 0.20 0.0 1.```
(edited)
Thats it. Then you will have ff99sb-ildn-nmr1.
Yay! I did it! I made the changes to the files and filenames and packaged up the following tar file:
ff99SB-ildn-nmr1.tar
Enjoy! --Vince
K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror and D.E. Shaw. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78:1950, 2010.
D.-W. Li and R. Bruschweiler. NMR-based protein potentials. Angew. Chem. Int. Ed. 49:6778, 2010.