[MMTK] a question about DNA and the Amber forcefield in MMTK

khinsen at cea.fr khinsen at cea.fr
Wed Sep 14 19:34:36 CEST 2005


On 14.09.2005, at 17:38, Kristina Woods wrote:

> (Pdb) p self
> Atom Na+.Na+
> (Pdb)
> ----------------------------------------------------------------------- 
> -----------------------------------------------
>  
> So I guess that it has something to do with the sodium ions in the  
> .pdb file.  I thought in Amber they were specified by Na+...but I  
> could be wrong and I will look it up.  Are they called something else  
> in MMTK?

The problem is not so much what they are called (the answer being  
nothing at all, as there is no definition of Na+ in the MMTK database)  
but how MMTK should map names in the PDB file to objects. All of this  
naming business in MMTK has nothing to do with how Amber does it. MMTK  
uses the Amber force field, but has no links to the Amber program.

To get your Na+ correctly defined, you need to do two things:

1) Create a database definition for Na+, i.e. a file called  
"Molecules/na+" in the database (preferably your own extension, i.e.  
~/.mmtk/Database/Molecules/na+). It should look like this:

name = 'Na+'
Na_plus = Atom('Na')
amber_atom_type = {Na_plus: 'na+'}
amber_charge = {Na_plus: 1.}

Please check the Amber parameters are right; I assume that the charge  
isn't.

2) Tell MMTK to create Na+ objects for residues called Na+ in the PDB  
file by changing the line

	universe.addObject(DNAconfiguration.createAll(None,1))

to

	universe.addObject(DNAconfiguration.createAll({'na+': 'na+'},1))


As you can see, the residue name enters in the last line, whereas the  
Amber atom type goes into the database file. All other names can be  
chosen as you wish.

Konrad.
--
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Konrad Hinsen
Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
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