PBrestraint Documentation

Installation

Running PBrestraint

Installation

1. Unpack the software

$ gunzip pbrestraint.tar.gz

$ tar xvf pbrestraint.tar

2. Enter the directory "pbrestraint" and edit Makefile

$ cd PBrestraint

$ vi Makefile

Instructions regarding editing Makefile are provided within Makefile

3. Run Makefile

$ make

4. File "pbrestraint.exe" should appear in the installation directory.

If installation failed, make sure that:

    a) Makefile is correctly edited, i. e. the correct directories and fortran flags were specified within Makefile;

    b) APBS 0.2.2 and CNS are installed on your system;

    c) you can compile APBS 0.2.2 and CNS that are installed on your system.

Running PBrestraint

Any original CNS input file can be used with the program:

$ pbrestraint.exe < minimization.inp

 

Requirements for running pbrestraint.exe with the Poisson-Boltzmann electrostatic restraint:

1. The input file should be edited so that it includes information regarding electrostatic restraint. There are two changes that should be introduced:

    a) the following patch should be inserted after parameter file initialization and before "xray" command:

        parameter

              nbonds

                repel=1.0

                eps = 1

                vswitch

                shift

                cdie

            end

        end

    The value of eps should be equal to that of protein dielectric which should also be specified in apbs.in (section 2).

    b) the following energy flags should be specified in addition to the existing ones:

    vdw pvdw elec apbs

Example of the input file with all required modifications is sample/cg.inp

 

2. File apbs.in should be in the directory in which the program runs.

This file contains Poisson-Boltzmann-restraint related parameters. Please note that the file consists of two similar parts. The ONLY difference between them is in values of solvent dielectric. Solvent dielectric in the SECOND PART should be equal to protein dielectric. Do not change settings for "calcenergy" anb "calcforce"`.

Example of the file is sample/apbs.in

Parameters are briefly explained in the comments given in apbs.in. Further details about the parameters can be found at the APBS web site.

 

 

ANDREI KOROSTELEV / MARCIA O. FENLEY / MICHAEL S. CHAPMAN;  Last updated 08/19/2004