If anyone knows about which software is good for creating a molecule , please let me know.
I have a moclule and I know the structure but i don’t have the coordinates for this molecule ,
So any help will be appreciated.
Go with Avogadro.
Avogadro is great for generating atomic coordinates.
You will still need to specify the partial charges of each atom, the bonds connecting them, angles, dihedrals, etc…, as well as the force-field parameters for this molecule. The number of parameters is large, and it’s difficult to do this by hand. Typically, most users will generate the angle, dihedral (improper) topology automatically and choose the force-field parameters using an established force-field, like OPLSAA, AMBER, COMPASS, GROMOS, PCFF, MARTINI, etc…
Check the list of molecule-builder tools at this
Some of these tools only work with a limited set of force-fields. I suggest you decide which force field you want to use before you decide which software tool to use.
Depending on which force field you chose, and which software you chose to generate the molecule, you might need to generate partial charges for each atom using a separate tool. The OPLSAA, COMPASS, and PCFF force fields include the partial charge of each atom in the force-field description. Amber (GAFF, GAFF2) does not, and you will have to generate the partial charges yourself. (Typically this is done using AmberTools, which is free.)
If you are at a university or academic institution, the ATB service is free.
P.S. I’ve been thinking about adding better LAMMPS as well as moltemplate export capability to avogadro, but I don’t know if the authors would accept the modification.
It should be noted here, that for reaxff calculations, and that is what this is likely about, NO bond topology information must be provided. Charges must be supported, but will be dynamically adjusted through the charge equilibrato.