[MMTK] Can MMTK handle neutral N-termini?

khinsen at cea.fr khinsen at cea.fr
Sun Oct 9 23:34:00 CEST 2005

On 05.10.2005, at 13:24, Dr. Seth Olsen wrote:

> Is there a way to make MMTK handle neutral N-termini?  I have  
> performed some Poisson-Boltzman calculations which indicate that  
> the N-terminus of my protein-of-interest is likely neutral at pH  
> 7.  I cannot find an entry in the database to the tune of  
> 'peptide_nt_neutral'.  Is there a workaround already or is that my  
> new job?

It's your new job :-)

The amino-acid varieties in the MMTK database are exactly those which  
are handled by the Amber 94 force field. The main work for adding  
other varieties is thus finding or calculating the force field  
parameters, in particular the partial charges for each atom. Creating  
the database files is then a rather straightforward procedure.

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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