ESP(1)

NAME

esp - calculate electrostatic potential

SYNOPSIS

esp -i dms_file [-o esp_file] [-q file] -a pdb_file [-r]

[-n] [-c cutoff] [-e epsilon] [-p len] [-v] [-w]

DESCRIPTION

Esp calculates the electrostatic potential of a solvent- accessible surface and stores it in an annotated ms surface file. This information can then be used by MIDAS to selectively color molecular surfaces based on electrostatic potential. Esp prints out a summary of the conditions used to calculate the potential.

-i dms_file

specifies a dms surface input file. The electrostatic potential is calculated for all points of this surface. Use the dms(1) program with the -n flag (to calculate normals) to generate dms_file. If the -p flag (see below) is given a value of 0, the normals need not be calculated by dms(1).

-o esp_file

indicates the annotated dms surface file to which the calculated electrostatic surface is output.

-q charge_file

The option -q charge_file supplies an alternate charge file for residue types. The default file used is /usr/local/midas/resource/charges.esp. Instructions for constructing alternate charge values are contained in the default file. The -q flag must precede the name of the Protein Data Bank format file (-a flag) to which the alternate charge file is applied. Thus, a series of command line parameters, -q file1 -a db1 -q file2 -a db2 may be used to associate alternate charge files with specific models.

-a pdb_file

is the name of the Protein Data Bank format file containing the coordinates for the associated dms surface file and any other atoms which should be included in the electrostatic calculation. The potential is calculated only for those surface points in dms_file, but all atoms in pdb_file are used in the calculation.

-r

indicates that the dielectric constant is dependent on the distance from the atom or charge to each surface point.

-n

specifies neutral spheres. Charges are summed within the cutoff radius defining the sphere, and an equal and opposite charge is spread uniformly across the sphere surface.

-c cutoff

indicates the cutoff radius in angstroms. The default value is 10.0.

-e epsilon

Epsilon is the dielectric constant, or if the -r flag is specified, epsilon is the factor that is multiplied by the distance in angstroms to give the effective dielectric. The default value is 1.0.

-p len

calculates the potential at a distance len angstroms from the surface. Positive values of len lie outside of the surface, while negative values lie within the surface. The default value of len is 1.4 angstroms.

-w

indicates that the electrostatic potential of each point should be appended to the corresponding line in the input dms_file.

-v

indicates verbose mode. Auxiliary information (e.g., the number of points found for each atom) is reported.

SEE ALSO

dms(1), midas(1) MidasPlus User's Manual

AUTHOR

Conrad Huang

UCSF Computer Graphics Laboratory

The idea of neutral spheres came from Paul Weiner while he was a graduate student in the Department of Pharmaceutical Chemistry, UCSF.