MIBPB: Matched Interface & Boundary method for Poisson Boltzmann

Software package for the estimation of electrostatic properties of biomolecules

1.	Introduction
	The MIBPB package is developed and compiled on Inter(R) Xeon(R) X5355. Electrostatic properties calculation of bio-molecules via the MIBPB package contains five steps: downloading or preparing protein PDB files; preparing protein structure; preparing protein molecular surface; generating molecular surface and Poisson-Boltzmann calculation. Each step is accomplished by certain package: protein structure is prepared by package PDB2PQR.py, molecular surface is prepared by script pqr2xyzr and molecular generation is done by MSMS. Generally the acceleration of the numerical calculation is collaborated with PETSc. For linear and nonlinear Poisson Boltzmann equation, the MIBPB package currently offers two types of solvers: the one-step solver which integrates all the above mentioned procedures, uses package default parameters and gives the result automatically; the half stand-alone solver which is only for PB calculation, users have to prepare the necessary files prior to the calculation but are able to adjust the parameters for each step, this gives much flexibilities for different purposes of calculation. In either way, user may need download or generate the PDB file first and save it with name in lower case.
2	Package unzipping and description
	After downloading the MIBPB package, users can decompress the zip file via following command:
	gunzip mibpb.tar.gz | tar xvf-
	the package contains 6 files, following are the description of those files:
	mibpb4.1.1		-----------------------one-step linear MIBPB solver
	mibpb4.1.2		-----------------------half stand alone linear MIBPB solver
	mibpb4.2.1		-----------------------one-step nonlinear MIBPB solver
	mibpb4.2.2		-----------------------halp stand alone nonlinear MIBPB solver
	pqr2xyzr		-----------------------protien molecuar surface preparation script
	1ajj.pdb		----------------------PDB file of protein 1ajj, example file
3.	One-step solver usage
	Prior to implement the one-step solver, the user may want to indicate the paths of the collaborating packages for PDB2PQR.py, pqr2xyzr and MSMS. Assuming they are installed or unzipped at the directories:
			/home/tools/pdb2pqr/
			/home/tools/MIBPB/
			/home/tools/msms/
	respectively. Then add the following into the .bashrc file (if b shell is used):
			export PDB2PQR_DIR=/home/tools/pdb2pqr/
			export PQR2XYZR_DIR=/home/tools/pqr2xyzr/
			export MSMS_DIR=/home/tools/msms/
			export PATH=$PATH:$PDB2PQR_DIR:PQR2XYZR_DIR:MSMS_DIR
	Then the user will be ready to run MIBPB solvers.
4.	Half stand-alone solver usage
	If users prefer to do the preparation themselves, then do the following:
		a.	Prepare the protein structure, command:
			pdb2pqr.py [options] --ff=<forcefield> <path> <output-path>
			where the <path> is the input PDB file and <output-path> is the output file, please save the output file in format as “pdbkey_apbs.pqr”. Users are able to choose the preferred force field (CHARMM or AMBER) and other options to deal with the structure. For more details, please consult : http://pdb2pqr.sourceforge.net/
		b.	Prepare the protein surface, command:
			pqr2xyzr pdbkey
			In this step, redundant information in “pdbkey_apbs.pqr” will be thrown away, the radius and charge information for each atom are recorded in “pdbkey.pqr” and “pdbkey.xyzr” files respectively. Please check the existence of the two files for future operations.
		c.	Generating molecular surface, command:
			msms –if pdbkey.xyzr -prob 1.4 –de 10 –of pdbkey
			where the probe radius used is 1.4 angstrom and triangle density is 10, those are also default parameters in one-step solver, users may adjust them upon different situations. After proper implementation, pdbkey.vert and pdbkey.face files are expected to be generated, which contain information about vertices coordinates and normal directions for triangles.
			Once the "pdbkey.pqr", "pdbkey.xyzr", "pdbkey.vert" and "pdbkey.face" for protein "pdbkey" are complete, users are ready to run the PB solver.
5.	Usage example
	There are fours solvers in this package, series mibpb4.1 are for linear PB equation while series mibpb4.2 are for nonlinear PB equation. Among each series, number 1 indicates that it is one-step solver while number 2 means that is half stand-alone solver. For example, to calculate for protein 1ajj via linear PB solver, input the command:
	mibpb4.1.1 1ajj eps1=2 eps2=80 h=1
	where eps1 is the dielectric constant for the solute and eps2 is the dielectric constant for the solvent, h is the grid resolution for the calculation. To calculate for protein 1ajj via nonlinear PB solver, input the command:
	mibpb4.2.1 1ajj eps1=2 eps2=80 kappa=0 h=1
	where eps1 is the dielectric constant for the solute and eps2 is the dielectric constant for the solvent, kappa is the modified Debye-Heckle parameter, h is the grid resolution for the calculation.
6.	Trouble shooting and bug report
	For most runtime error, the solver will print corresponding information on screen to fix it. For others or bugs showing up during the calculations, please report your problem to:
	wei@math.msu.edu

[Michigan State University]

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