[MMTK] the modified nucleotides in MMTK

Konrad Hinsen research at khinsen.fastmail.net
Wed Jan 5 13:04:37 UTC 2011


On 5 Jan, 2011, at 12:40 , LIU Changdong wrote:

>  I'm a fresh hand in MMTK and planning to refine a  tRNA model which contains the modified nucleotides.
>  The model was generated by ModeRNA.
>  MMTK discarded the  the modified nucleotides during refinement.
> Although I got the parameter files for  the modified nucleotides in Amber format, I read though the manual and
>  had no idea how to use and where to put the parameter files in MMTK.
> 
> Would you please give any suggestions?

Please look at this section of the manual:

	http://dirac.cnrs-orleans.fr/Manuals/MMTK/mmtk.html#constructing-the-database

What you need to do to use modified nucleotides is:

1) Create a group definition file for each nucleotide type (using the standard ones as a starting point).
  The group definition file contains everything there is to know about the nucleotide, in particular the force field parameters (atom type and charge).

2) Put this file into a directory that is on the database search path.
  The easiest choice is $HOME/.mmtk/Database/Groups

3) In the Python script that makes use of the modified nucleotides, add the lines

	from MMTK.Biopolymers import defineNucleicAcidResidue
	defineNucleicAcidResidue('my_new_nucleotide', 'dx')

  The first argument is the name of your group definition file, the second one the PDB code you want to associate with that residue.

Note that you must provide 3-ter and 5-ter versions of your residue explicitly if it can occur in a terminal position.

If your residues require specific Amber parameters, i.e. if they use atom types that are not in the standard Amber set, you need a modfile in Amber format and pass its name to the Amber99ForceField constructor:

	http://dirac.cnrs-orleans.fr/Manuals/MMTK/modules.html#module-MMTK.ForceFields.Amber.AmberForceField

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
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