README

This is the startup project of TPPMKTOP utility for generating molecular
dynamic topology directly from the chemical structure file.

== INSTALL ==

Install mysql++, boost and openbabel. Project tested with openbabel-2.4 (install it by hands).

For ubuntu:20.04 these libraries are required:

apt-get install -y \
  libmysqlclient21 libmysql++3v5 libboost-thread1.71.0 libboost-filesystem1.71.0 \
  libboost-program-options1.71.0 libboost-regex1.71.0 libboost-log1.71.0 \
  libmysql++-dev libboost1.71-dev libboost-thread1.71-dev libboost-filesystem1.71-dev \
  libboost-program-options1.71-dev libboost-regex1.71-dev libboost-log1.71-dev

To install run from folder:
                   
./bootstrap.sh
OPENBABEL_CFLAGS=-I/usr/local/openbabel-240/include/openbabel-2.0/ \
 OPENBABEL_LIBS=-Wl,-rpath=/usr/local/openbabel-240/lib \
 LDFLAGS=-L/usr/local/openbabel-240/lib ./configure
make && make install

== DESCRIPTION ==

There are two working programs now:

* TPPRENUM

tpprenum renumerate molecule using the longest tail algorithm. Some branched
molecules are numerated with *tpprenum* well. Highly connected molecules (such
as graphene layer or fullerene) could not be renumbered by this algorythm.

* TPPMKTOP

This utility uses SMARTS patterns defined in the Database to attribute atoms in
structure with corresponding correct atomtypes of the force field. The rest
interactions (bonded and non-bonded) are generated further according to
attributing atomtypes.

TPPMKTOP/TPPRENUM are now located at the website:

http://erg.biophys.msu.ru/tpp

Please read the description here:

http://erg.biophys.msu.ru/wordpress/archives/32

and write email at == comconadin (at) gmail (dot) com == if you have questions
about usage of tppmktop or collaboration, etc.