[AMBER] Parametrisation of Silicon based molecules for Amber simulations ?

From: Marek Malý <maly.sci.ujep.cz>
Date: Thu, 19 Mar 2009 23:49:21 +0000

Dear Amber users,

I would like to simulate molecules which contain also Si (silicon) atoms.
Please see attached fig. "mol01.jpg" or "mol.pdb."

I tried to parametrise small "testing" molecule using Antechamber and
I have obtained relevant PREPIN ("mol.prepin") and FRCMOD ("mol.frcmod")
files.
The prepin file is OK and also "Si" atoms were asigned with calculated
partial charge etc.

But there is problem with FRCMOD file which should be probably interpreted
in this case only as
an empty template for proper forcefield parameters (bond, angle, dihedrals
parameters) which
need to be included "manually".

Nevertheless I tried to make PRMTOP and INPCRD file (just for the
curiosity) and I succeeded,
but after reading of this two files by "Chimera" and labeling the element
types, the "Si" atoms
were asigned with the "LP" label (please see "mol02.jpg") although in
PRMTOP file are all "Si" atoms
named properly and in section "FLAG AMBER_ATOM_TYPE" is clearly written
type "Si". But this is probably
question for "Chimera" forum :))

It is clear to me that I will have to find a proper forcefield parameters
so
I am kindly asking for any info, links to relevant databases etc.

For example I succeed to simulate this molecule in vacuum with MS software
using "Dreiding" forcefield.
Could be a good idea to adopt desiderative parameters from this forcefield
and incorporate them into my FRCMOD
file ?

How to decide between for example two slightly different parametrisations
which I could find in different data sources ( articles, databases ) ?
Is there any highly recommended forcefield database available ?


I appreciate any help and advices especially from the experienced
researchers.


Thank you very much in advance !

             Marek

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Received on Fri Mar 20 2009 - 01:18:08 PDT