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

  • The QM for ligand option in BUSTER uses by default a helper executable using the fdynamo library. We would like to thank Prof. Martin Field for permission to distribute the helper with BUSTER.
  • By default BUSTER calls the helper with a method 'AUTO' the helper then selects the semi empirical model to be used according to the atomic numbers of the atoms supplied. The first method that treats all element types in the supplied molecule is selected from the list:
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
  • To PM3 or AM1 in preference to RM1 you can use -qm_method PM3 command line option (although this generally not a great idea).

MOPAC2009 helper script

  • MOPAC2009 is the latest version of MOPAC, the most popular semi-empirical quantum package. MOPAC2009 implements PM6 method that can handle most element types.
  • notes:
    • Thank you to Prof. Jimmy Stewart for providing us an evaluation copy of MOPAC2009
    • you may have to edit the helper script to localize it for your location .
    • remember to set permissions for the script so that it can be executed after you download it:
chmod a+x  gelly_qm_helper_mopac2009.pl
    • The helper can be invoked by autoBUSTER refine using the -qm_helper command line argument.
    • The default (AUTO) method is PM6.
    • We are currently evaluating how to best use MOPAC2009 and PM6.

GAMESS helper script

  • GAMESS is an excellent quantum chemistry program maintained by the Gordon research group at Iowa State University. "A site license for GAMESS is available at no cost to both academic and industrial users".
    • Although semi empirical quantum methods are reasonably accurate, ab initio and DFT methods can be more so (but are much more computationally expensive).
    • Please refer to the GAMESS homepage for details of how get a license, download and setup GAMESS.
    • Please make sure the GAMESS script rungms works properly before trying to use it with BUSTER. In case it helps our localized version of the GAMESS rungms script can be downloaded here: rungms.
  • The latest version of a helper that uses GAMESS:
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
  • notes:
    • you will have to edit the helper script to localize it for your location (like the GAMESS).
    • remember to set permissions for the script so that it can be executed after you download it:
chmod a+x  gelly_qm_helper_gamess.pl
    • The helper can be invoked by autoBUSTER refine using the -qm_helper command line argument.
    • The default (AUTO) method is HF/3-21G(d)_pcm. This is a small basis set ab initio method and PCM water is used to reduce the electrostatics. This method has yielded good results in initial tests, see 2qxs tutorial example.
    • For testing to get the script working it is sensible to use -qm_method AM1 for speed.
    • The use of the GAMESS helper is illustrated in the 2qxs tutorial example.

Gaussian g03 helper script.

  • Gaussian is a very popular and widely used quantum chemical program. See http://www.gaussian.com/
  • Because of user demand, we have prepared a helper script for Gaussian g03:
    • gelly_qm_helper_gaussian.pl tested version 28.07.12
    • remember to set permissions for the script so that it can be executed after you download it:
chmod a+x  gelly_qm_helper_gaussian.pl

OpenEye helper programs

  • OpenEye http://www.eyesopen.com/ have written helpers programs for MMFF94, AM1 and PM3.
  • The MMFF94 force field helper can be used through the -forcefield option and provides new capabilities, see AutobusterLigandForcefield No additional scripts are required.
  • The first version of the helpers v 2.3.0.4 truncated coordinates to a limited number of figures on read. This will be fixed on the next release. It has a little effect on practical applications.

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

  • The command line options for using a helper that invokes 3rd party QM software are long and not easy to remember!
  • the autoBUSTER user-created macro feature is designed to help with exactly this kind of thing. It is explained in detail in the documentation online or in you local documentation that can be located using refine -h
  • for example we will create macros to use the GAMESS helper script as installed at Global Phasing with the what we find to be the most useful QM representations.
  • first make sure that the QM software and helper are correctly installed and working, for instance by running the test.
  • Create a directory to contain the macros. This directory should be separate from the BUSTER distribution. Here we use the directory /home/osmart/qmmacros
  • In this directory use your favorite editor to create a macro like:
vi gamessHF321.macro
    • file contents
# 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"
    • gamessHF321.macro
    • clearly your macro will need to be adapted for your site and QM helper!
    • In practice it would be sensible to create a number of macros with different QM options and/or helpers.
  • To use the macros with refine set the environment variable autoBUSTER_MacroDirs to the directory name containing the macros. Exactly how you do this depends on what shell you use. For tcsh type or include in ~/.cshrc or ~/.login:
setenv autoBUSTER_MacroDirs /home/osmart/qmmacros
    • for bash shell
export autoBUSTER_MacroDirs=/home/osmart/qmmacros
  • Once you have done this, the macro(s) should be usable in refine. A good check is to list the available macros by refine -M list:
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 

  • Then to use the macro issue its name after -M, for example to use the GAMESS HF321 macro for a neutral ligand with 3 letter code INH use the option
refine -p in.pdb -m in.mtz -d 01 \
 -qm LIG -M gamessHF321 > 01.log &

Methanol gradients test for helper scripts

  • To check that a helper script is working properly it is useful to runs check on a small molecule. In particular it is important for the helper to provide the correct gradient vector (minus the force). This can be checked by comparing the vector with numerical derivatives, calculated by the central differences method.
  • Here we use methanol - download the pdb and cif files:
  • Then download the check helper script and adapt it to test your helper:
  • results for comparison
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

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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