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1. Introduction

The MolEdit is small service that allows to draw a 2D structure thanks to the Ketcher applet, to perform a conversion to 3D (provided by AMMP molecular mechanics software) and to save it in any molecule format supported by VEGA.


2. How it works

The edited molecule is read by VEGA that performs the following steps:

  1. if needed, add the hydrogens;
  2. assign the atom charges (Gasteiger - Marsili method);
  3. save the molecule in the AMMP file format.

AMMP optimizes the structure in two steps:

  1. distance geometry optimization by Gauss - Siedel algorithm (15 steps);
  2. conjugate gradients minimization (100 steps, toler = 0.01).

The minimized structure generated by AMMP is read by VEGA and converted to the file format requested by the user. Finally, it's sent to the user.
The optimization phase isn't completely exhaustive because 100 steps could be not enough to optimize big molecules.


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