BUSTER -forcefield option

Introductory tutorial on 2i0g.



Starting Files

fetch_PDB 2i0g
grade_PDB_ligand I0G

(A) Preparation: add hydrogen atoms to the ligand(s)

hydrogenate -p 2i0g/2i0g.pdb -l I0G.grade_PDB_ligand.cif 
-ligonly -zero -o 2i0g_addhI0G.pdb

(B) Refine with -forcefield I0G -l I0G.grade_PDB_ligand.cif

time refine                 \
-p 2i0g_addhI0G.pdb         \
-m 2i0g/2i0g.mtz                 \
-autoncs                    \
-l I0G.grade_PDB_ligand.cif \
-forcefield I0G             \
-d partBff -report > partBff.log &
firefox partBff/01-BUSTER/Cycle-1/LIST.html
 QM_HELPER_LOG: forcefield.pl invoking OpenEye Helper with /mnt/software/GPhL/ALL_snapshot_20131118/scripts/qm-mm-helpers/OpenEye.pl 0 1 AUTO
QM_HELPER_LOG: gelly helper script to run OpenEye helpers for force field or QM energy/gradient calculation
QM_HELPER_LOG: Please obtain helpers for OpenEye http://www.eyesopen.com/
QM_HELPER_LOG: helper script location /mnt/software/GPhL/ALL_snapshot_20131118/scripts/qm-mm-helpers/OpenEye.pl
QM_HELPER_LOG: picked up charge=0 multip=1 method=AUTO from command line
QM_HELPER_LOG: Open Eye executable used:  /software/OpenEye/openeye/bin/buster_helper_mmff
QM_HELPER_LOG:            :jGf:
QM_HELPER_LOG:         :jGDDDDf:
QM_HELPER_LOG:     ,fDDLt:   :iLDDL;
QM_HELPER_LOG:   ;fDLt:         :tfDG;
QM_HELPER_LOG: ,jft:   ,ijfffji,   :iff
QM_HELPER_LOG:    ;DDDj         tDDDi
QM_HELPER_LOG:    ,DDDf         fDDD,         Copyright (c) 2013
QM_HELPER_LOG:     LDDDt.     .fDDDj          OpenEye Scientific Software, Inc.
QM_HELPER_LOG:       :ifGDDDDDGfi.            Version:
QM_HELPER_LOG:           .:::.                Built:   20130710
QM_HELPER_LOG:   ......................       OEChem version: 1.9.2 20130710
QM_HELPER_LOG:   DDDDDDDDDDDDDDDDDDDDDD       Platform: Ubuntu-12.04-g++4.6-x64
QM_HELPER_LOG: Input ISM: c1cc(ccc1C2C3CCCC3c4cc(ccc4O2)O)O
QM energy for QMset    1 picked up as            870.70907
QM_HELPER_LOG: Input ISM: c1cc(ccc1C2C3CCCC3c4cc(ccc4O2)O)O
graph_autobuster_QM -d partBff -k -qmzero 0 -launch
visualise-geometry-coot partBff

(C) Control refine with dictionary

time refine                 \
-p 2i0g_addhI0G.pdb         \
-m 2i0g/2i0g.mtz                 \
-autoncs                    \
-l I0G.grade_PDB_ligand.cif \
-d partC -report > partC.log &
time refine                 \
-p 2i0g_addhI0G.pdb         \
-m 2i0g/2i0g.mtz                 \
-M MapOnly                  \
-l I0G.grade_PDB_ligand.cif \
-d MapOnly -report > MapOnly.log &

(D) Analysis comparing the Force Field, QM and dictionary refine jobs

What MapOnly part C GRADE part B -forcefield I0G part B -qm I0G
Ligand representation PDB GRADE dictionary MMFF94 RM1 semi-empirical QM
Rwork 0.2297 0.2154 0.2160 0.2161
Rfree 0.2663 0.2500 0.2501 0.2505
MolProbity overall score 2.40 1.44 1.39 1.34
What MapOnly part C grade part B -forcefield I0G part B -qm I0G
Ligand representation PDB GRADE dictionary MMFF94 RM1 semi-empirical QM
Map correlation coefficient CC(2Fo-Fc) 0.953 0.952 0.952 0.949
Mogul number of bad bonds 2 0 0 0
Mogul bonds RMS Z 2.5 0.3 1.0 1.0
Mogul angles RMS Z 0.8 0.4 0.7 1.3

(E) Assessing ligand strain local conformation energy and motions for the refinement using MMFF94

   egrep "I0G A|CRYST1" partBff/refine.pdb > partBff.IOGA.pdb

gelly_refine -p partBff.IOGA.pdb \
    -l I0G.grade_PDB_ligand.cif -forcefield I0G \
   -d partEff -o partEff_out.pdb \
   -max 1000 -glim 0.01 -jiggle_xyz 0.1 > partEff.log &

graph_autobuster_QM -d partEff -k -q 0
 final raw QM energies   =   263.77 kJ/mol

graph_autobuster_QM -d partBff -qmzero 263.77 -k
# -qmzero specified so report QM energies relative to 263.77
# kcal set scale energies by 0.238845896627496
#       5      63     357           1.73           1.73

partBff_distances.png partEff_distances.png
refined ligand has short contacts these are relieved on relaxation with MMFF94

Back to Ligand QM/force field top index page

Page by Oliver Smart and Ian Tickle 18 Nov 2013. Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com