Dear Antonio,
> 1. Copy the library file “nucleic12.lib” in
> “/amber18/dat/leap/lib/nucleic12.lib” and rename it to RNA.lib
>
> 2. Delete all entries that include DNA (*i.e.* I think delete all the
> one that starts with “D***”)
I think it's easier to copy library "RNA.lib", which is already present in the amber18 package, than modifying the nucleic12.lib, because you don't need to further modify the file...
I didn't check very carefully (I've just looked one residue) but I think the partial charges and atom types for RNA in both libraries are the same... (check it yourself!)
> *1. **Do the charges in the article table correspond to “Atom name”
> column or “atom type” in the .lib column?*
Charges are set by "Atom name", which means to the very specific atom... if you check the RNA library you'll notice that there is no atom-type "N4" in residue "C" nor "N1" in residue "A" (to give you some examples)... in that way the electrostatic interactions are decoupled from other parameters defined the atom-types (Lennard-Jones, bonds... etc)
> *2. **Is the atom type between RNA and DNA redundant? If yes, do you
> have any idea how to distinguish between RNA and DNA?*
I don't understand what do you mean with this... The very central idea in a force field is having a reduced set of atom-types which are hopefully transferable between molecules because what matters is the chemical context (functional group) and not the molecule type... except for partial charges which allows you for some specificity to the molecular context...
If for some reason (e.g. special bond terms) you need residue specific atom-types, then you will have to create new atom-types for those residues...
Best,
Matías
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Antonio Amber Carlesso" <antonio.amber.carlesso.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
CC: "Johanna Hörberg" <joohannah93.hotmail.com>
Enviados: Jueves, 16 de Agosto 2018 5:57:47
Asunto: [AMBER] implement_revised_RNA_force_field_general rule?
Hi all,
We are trying to implement the revised Tan, Piana, Dirks and Shaw RNA force
field in Amber (
https://doi.org/10.1073/pnas.1713027115 ) .
I will briefly share with you our step, in order to receive some more
comments and insightful comments and also hopefully give a sort of overview
that could be useful to someone..
What we should do is add the modified electrostatic, vdW, and torsional
parameters in the AMBER ff14 RNA force field
*LIB file:*
1. Copy the library file “nucleic12.lib” in
“/amber18/dat/leap/lib/nucleic12.lib” and rename it to RNA.lib
2. Delete all entries that include DNA (*i.e.* I think delete all the
one that starts with “D***”)
3. Modify the charges
*Just a couple of questions:*
*1. **Do the charges in the article table correspond to “Atom name”
column or “atom type” in the .lib column?*
*2. **Is the atom type between RNA and DNA redundant? If yes, do you
have any idea how to distinguish between RNA and DNA?*
*FRCMOD file:*
1. Add revised dihedral angle
2. Add revised vdW parameters
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 16 2018 - 08:30:02 PDT
