CCL: Forcefield parameters transformation - derivation ?
- From: Marek Malý <marek.maly#%#ujep.cz>
- Subject: CCL: Forcefield parameters transformation - derivation
?
- Date: Mon, 06 Apr 2009 17:37:59 +0200
Sent to CCL by: =?iso-8859-2?Q?Marek_Mal=FD?= [marek.maly===ujep.cz]
Dear all,
I would like to simulate carbosilanes and later their complexes with
organic macromolecules using Amber software.
Unfortunately Amber forcefields do not contain proper ff parameters
for
silicon.
In spite of this fact there is still possibility to simulate my
Si-based
molecules in Amber
but I have to find proper parameters (e.g. bond, angle, dihedral)
somewhere elsewhere ...
I need ff parameters for Si in this contexts:
C-C-C-Si, Si-O-C-C, C-Si-C-H etc.
So I see here two solutions:
A)
To import relevant parameters from another forcefields like CVFF,
PCFF,
MM2, MM3 ...
Regarding to this point it would be nice to have some routine which
could
be able to convert
one forcefield file XYZ to ff file written in Amber format. If possible
not to
transform just text formating of the source XYZ ff file with respect of
Amber formating,
but also to transform properly the parameters values with respect to
eventual diferences in units or analytic
formulas for interatomic forces.
B)
To derive all the necessary parameters using some intelligent
(probably
quantum mechanics based) software which could be able
to do this analysis for small residua provided for example in PDB
format.
Again would be nice to have this parameters
in format compatible with Amber ff.
I am kindly asking for any (even only partial) information regarding
to
this topic or just for redirecting to
relevant information resources. Of course that I will be grateful not
only
for info related to some appropriate SW
which can help me regarding to A) or B) but I will also appreciate any
info based on own experiences, strategies, suggestions, warnings ...
regarding to this topic.
Best regards,
Marek
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