Editing MACROMODEL

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MacroModel is an integrated software system from Schrödinger, Inc. for modeling organic and bioorganic molecules using molecular mechanics. It is the generic term used to describe several programs and it can be used within Maestro.

BatchMin is the batch-mode molecular modeling computation facility for use with MacroModel.  It is designed to minimize the energy of one structure or a series of structures, to eliminate duplicate conformations, to do conformational searches and to conduct molecular dynamics simulations. BatchMin may be configured to run on the same system as the front-end visualization tool or remotely via several network protocols. Batchmin may also be run via a command line or via a batch queuing system.


To submit Macromodel input files in kimik, you will need to use the job_type '''bmin''' (i.e. qs 1 s bmin input.com)


Manual  [http://10.0.7.240/wiki/images/files/jaguar/mm85_user_manual.pdf]


==Super-Short guide to MACROMODEL for beginners (by Luca)==
 
*  [[Image:Macromodel.pdf]] 



==Links==

http://www.schrodinger.com/ProductDescription.php?mID=6&sID=8

http://www.chem.purdue.edu/computation/MacroModel.htm

== Recommendations when using Macromodel ==

* Use a "nice" Force Field i.e. MM3

* Chose a "nice" CSearch Method, i.e. LowMode sampling

* Use '''Comparison Atoms''' tool to avoid having repeated structures. Default options use all atoms, select only those that are really important (the skeleton of the structure). Changes on the rest of atoms will induce changes on the skeleton. i.e for Ph3C-CH2-CPh3 the skeleton will be 1 carbon of each Ph (the one bonded to the sp3 carbon) and the central atoms C-C-C.

* Have a LOT of patience...

==Macromodel related tips==

* Changing the force field in Maestro you may have other atom types available.

*  [[Incorporating Metal Atoms and Building Complexes]]

*  [[Monte Carlo Conformational Search]]

* [[Xcluster]]

==Scripts==

* [[Macromodel_to_gaussian]]