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MOPAC-En UK Quick Guide
MOPAC-En UK Quick Guide
GNORM=20 GEO_REF="SELF".
COPYRIGHTS
Use MOPAC to add all hydrogens: copy the PDB file to a .MOP
file and run MOPAC. If you need to use additional keywords, add MOPAC: is a trade mark of and by James J. P. Stewart
three lines before the PDB file and use the first line to enter your <MrMOPAC@OpenMOPAC.net>.
keywords and ADD-H.
CITATION: MOPAC2012, James J. P. Stewart, Stewart Computational
Run a calculation with keywords CHARGES RESIDUES. Verify Chemistry, Colorado Springs, CO, USA, http://OpenMOPAC.net/ (2012).
that all residues have the expected number of hydrogen atoms.
THIS DOCUMENT: was written and designed by Jos R. Valverde from
the Spanish EMBnet node (CNB/CSIC) and is being distributed by
Run an intial optimisation on the H atoms only using NOOPT EMBnet's P&PR Committee.
OPT-H GNORM=20.
Check the ionisation states: look for ANION and CATION entries. work. Many countries have national or local nodes providing training
Verify salt bonds and that, for every ion, there is a counterion courses and other forms of help for users of bioinformatics software.
nearby. Check potential H-bonds. Ionise "by hand" any needed Find more information about your nearest node from EMBnet's web site:
groups (e.g., phosphates) using SITE. Correct bond orders using
SETPI, and eliminate spurious bonds with CVB.
http://www.embnet.org/
It may be helpful to run a 1SCF calculation to compute properties
and a RESEQ calculation to reorder atoms as expected by PDB.
MOPAC