How to use

1) I want to use mol2 files provided in the links:

You can use mol2 structure files, provided in the links, directly in AMBER. These mol2 files are final structures obtained after MD simulations (see corresponding references) and the initial coordinates were obtained by using residue libraries with the help of DBT. The mol2 file contains charges, GAFF atom types. So these can be used directly in AMBER simply as follows:

In your terminal type xleap (or tleap)

in xleap window type these

source leaprc.gaff

var = loadmol2 YOUR.mol2

Later you may proceed as you like (adding solvents, ions, salts etc. So you need to load corresponding solvent and ions libraries as well)

2) I want to build my own dendrimer initial coordinates and generation:

You can also build your own dendrimer (generation) using libraries provided in the links on Home page. This way you can get initial starting coordinates that can be later used with force fields of your choice, though DBT provides directly usable GAFF files. For this you can see Tutorial.

BE CAREFUL: There are different libraries for different dendrimer and different protonation states. Its always a good idea to see references provided and once you obtain the structures you can see number of atoms matching with the reported structures! Even if you have minor doubt regarding information provided and usage, do not hesitate to mail dbt.query (aT) gmail.com OR maiti [a] physics.iisc.ernet.in