User talk:Kitus1444/sandbox

Tested Platforms
Molden program has been tested on different platforms, namely: -Linux -Windows NT / Windows95 / Windows2000 / WindowsXP -Native windows version -MacOSX -Silicon Graphics IRIX -Sun SunOS and Solaris

AMBFOR module for optimizations
Ambfor is the main force field module of Molden, but it is not an internal program, in fact, is an external program that can be initialized from Molden. Ambfor admits protein force field Amber and GAFF (General Amber Force Field).

Use of Ambfor is automatically when a protein is studied with Molden, and depending on the molecule size it is also possible to use GAFF force field (only small molecules). No matter which method we use as Amber and GAFF are based on atomic charges, main differences are encountered in the computational cost, GAFF is very expensive. For system where GAFF force field is recommended instead of Amber, for example systems with quantum chemically derived charges, there is another option to decrease the computational effort, use semi-empirical derived charges (MOPAC) with correction sheme, AM1BCC.

Molden maximum number of orbitals
This paragraph, only has to be taken into account if you are using older version of Molden (3.5 or older) because these versions use static memory allocation for orbitals, instead of dynamic. “Exceeding MaxNum of orbitals!” If we obtain this error message means that our system has more than 256 orbitals and 150 atoms, because Molden has these maximum values by default, but it can be solved going to source directory and applying a script named “change_parameter”.

Crystalline structure
Molden can read the following file formats with crystal information:

-FDAT -CSSR -CAR -MSF -Mol2 -ShelX -MSI -CONTCAR

But this is not the only function available in Molden, there is a procedure to create it from scratch, using the z-matrix builder and adjusting cell parameters. To finish, just save your crystal structure with one of the following formats:

-Mol2,MSF,CSSR,MSI.