Subject: charmm problems

From: Santiago Cuesta <[email-masked]>
Date: Tue, 25 Jun 2002 13:18:37 +0200

Hi Alice !

1) One way to balance charge is adding Na+ to your system. In your case ...9 
Na+ ...
... how to add  in CHARMM is easy, but WHERE to add it's a problem ... One 
possibility is to place the ions close to the charged residues, making sure 
that there is no overlapping with the protein.

I prefer to make a little script that generates ions at random positions , 
then I use some criteria to accept them or not (like electrostatics, overlap, 
etc ...). After that,  I think it's a good strategy to complete the 
neutralization performing a short  "equilibration". (fix the residues, and 
allow the ions and solvent to accomodate).

2) y 3)  Maybe these references will help you to understand minimization and 
dynamics analysis:

To begin understanding CHARMM and molecular simulations search in the net 
these :

"Übungen zu NMR-Spektroskopie und Biomolekularer Simulation" by Stefan 
Boresch (1999)  (It's in english)

" Introduction to Macromolecular Simulation"  by Peter J. Steinbach 

Good tutorials are:

http://www.ch.embnet.org/MD_tutorial/
http://www.sinica.edu.tw/~scimath/msi/insight2K/charmm_principles/Ch04_mol_dyn.FM5.html#678970

I hope last one will answer all your problems.

Finally you can find some charmm examples in:

http://www.psc.edu/general/software/packages/charmm/example_input/

Bye !!

Yours Sincerely

Santiago Cuesta

------------------------------------
Santiago Cuesta López
Dep. Física de la Materia Condensada.
Grupo de Simulación de Sistemas Complejos
Universidad de Zaragoza. (Spain)

e-mail: [email-masked]