Direct use of weighted Quantum Chemical Energy for ligands in BUSTER refinement:

QM helper applications

As described in the Introduction to the method page BUSTER uses helper executable invocations to evaluate the potential energy and its gradients for any given ligand position. This page provide the source code and technical details of the helpers.

contents


fdynamo helper executable distributed with BUSTER

RM1 H C N O F P S Cl Br I
PM3 H Be C N O F Na Mg Al Si P S Cl K Zn Ga Ge As Se Br Cd In Sn Sb Te I Hg Tl Pb Bi
AM1 H Li Be B C N O F Na Mg Al Si P S Cl K Zn Br I

MOPAC2009 helper script

chmod a+x  gelly_qm_helper_mopac2009.pl

GAMESS helper script

Date Improvement
2011-04-15 use multiple processors for GAMESS
2011-04-17 GAMESS can only use one processor for AM1
2011-05-17 Add PCM option to reduce electrostatics
chmod a+x  gelly_qm_helper_gamess.pl

Gaussian g03 helper script.

chmod a+x  gelly_qm_helper_gaussian.pl

OpenEye helper programs


Using autoBUSTER refine macro feature to make using QM helper easier for users

vi gamessHF321.macro
# use GAMESS qm helper using HF/3-21(d) with pcm water
# you will algamessHF321.macroso need to specify residue like "-qm LIG" 
#                              or if charged "-qm XXX+1"
+BusterExtraArgs="-qm_method HF/3-21G(d)_pcm -qm_helper /home/osmart/autobuster/gelly/helpers/gelly_qm_helper_gamess.pl"
setenv autoBUSTER_MacroDirs /home/osmart/qmmacros
export autoBUSTER_MacroDirs=/home/osmart/qmmacros
refine -M list

--------------------------------------------------------------------------- 
 Macro name               Description
 --------------------------------------------------------------------------- 
 
edited 
 gamessHF321           :  use GAMESS qm helper using HF/3-21(d) with pcm water
                          you will also need to specify residue like "-qm LIG" 
                                                       or if charged "-qm XXX+1"
edited 

refine -p in.pdb -m in.mtz -d 01 \
 -qm LIG -M gamessHF321 > 01.log &

Methanol gradients test for helper scripts

program method function value Grms gradient angle (degs) gradient difference/gradient average
fdynamo AM1 -2861.98 926.233 3.4151E-06 5.7103E-08
GAMESS AM1 -6.257352E+05 926.405 3.5959E-03 6.4043E-05
OpenEye AM1 v 2.3.0.4 -2859.95 926.714 7.2999E-02 1.2878E-03
GAMESS HF/6-31G(d) -3.887490E+06 1030.77 3.2555E-03 5.7400E-05
Gaussian g03 HF/6-31G(d) -3.887490E+06 1030.77 5.9841E-02 1.0491E-03
OpenEye MMFF v 2.3.0.4 104.128 540.555 7.5542E-02 1.4007E-03
OpenEye MMFF v 2.3.1.b.2 104.128 540.554 1.2074E-06 1.8230E-09

Back to Ligand QM/force field top index page

Page by Oliver Smart first version 03 Feb 2011, updated many times last 26 November 2013. Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com