Effective Charge Method

Calculation of effective charges. More...

Functions/Subroutines
program	ecm_all
	Create effective charges in one step. More...
program	ecm_expand
	Make the regularization step. More...
program	ecm_mkreglev
	Create the effective charges. More...
program	ecm_mksites
	Make the test charges. More...
program	ecm_regularize
	Make the regularization step. More...

Detailed Description

Calculation of effective charges.

This additional information are writen in ecm_all.f90

A step by step construction of the effective charges require 4 steps :

• ecm_mksites : make the test charges ( in a *.tcha file ) from the pdb. Hardcoded approximative values are assigned to some atom ( eg : oxygens of lysines have -0.5 e )
• ecm_expand :
• ecm_regularize :
• ecm_mkreglev : given a criteria, will compute the effective charges at a specific iteration

The advantage is a better control at the different steps. It allows to choose precisely the level of iteration to stop

This can be done in one step with :

• ecm_all : call the 4 previous steps and generate directly the effective charges

The advantage : easier to use

To be reusable, the 4 steps are writen in 4 main subroutines ( sub_mksites, sub_expand,.. ), implemented in ecm_mainsubroutine.f90

If your system contains unknown atom or residue type, you should use an external file: add_atoms (see examples)

Function/Subroutine Documentation

ecm_all()

program ecm_all

Create effective charges in one step.

Make all steps for computing the effective charges
Call subfunctions of the different steps

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ecm_expand()

program ecm_expand

Make the regularization step.

make ecm_regularize in ecm_expand, anyway always read the same matrix, no option possible
make ecm_mkreglev in ecm_regularize, need option
should add option if we want to write the intermediate matrix
will sub_expand will call sub_regularize if need to split after

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ecm_mkreglev()

program ecm_mkreglev

Create the effective charges.

Last step in the process

Recreate effective charge from the computed matrix
Similar to ecm_regularize, but stop at a particular iteration in the regularization

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ecm_mksites()

program ecm_mksites

Make the test charges.

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ecm_regularize()

subroutine ecm_regularize

Make the regularization step.

Make the complete iteration
Then need to call ecm_mkreglev to choose a particluar iteration

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