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from the AmberTools program (free of charge) and (ii) AMBER
program; then run the command:
antechamber –i IRB.pdb –fi pdb –o IRB.com –fo gcrt
Note: For the required calculations, the use of AMBER and
Gaussian is not restrictive; other appropriate molecular modeling and QM packages may be used as well.
2. Install and compile Gaussian; run Gaussian (on Linux/Unix
environment) for geometry optimization of IRB and for electrostatic potential (ESP) generation:
g09 IRB.com > IRB.log
The input file (IRB.com) for Gaussian calculations is shown
in Note 1. Output IRB.log contains the optimized structure of
IRB and information regarding ESP.
Note: Most of the output files produced by Gaussian and
AMBER regarding this case study are very large and therefore
are not presented here.
3. Generate charges according to the restrained electrostatic
potential (RESP) method with ANTECHAMBER. The geometry of IRB and the RESP charges are included in the IRB.mol2
output file:
antechamber –i IRB.log –fi gout –o IRB.mol2 –fo
mol2 –c resp
4. Generate missing parameters for IRB with the parmchk routine
of ANTECHAMBER:
Fig. 3 Schematic workflow for systems’ preparation for MD simulations
Georgios Leonis et al.