Dear, amber users.
# Short
My question is "How to assign 'sigma (A)' parameter of TIP4P-XXX water
model in Amber 14"
('sigma [A]' is described in
http://www.sklogwiki.org/SklogWiki/index.php/TIP4P-Ew_model_of_water)
# Detail
I would like to use a TIP4P-D model (1) which is derived from a
TIP4P-2005 model (2). So I decide to create a forcefield and parameter
files of TIP4P-2005 model in the beginning.
I found an amber mailing list archive which explain where the TIP4P-EW
parameters are defined (
http://archive.ambermd.org/201310/0410.html) so
I checked the following files
- `dat/leap/parm/frcmod.tip4pew`
- `dat/leap/lib/solvent.lib` (`!entry.T4E.unit.xxxx` sections)
And I found that the following parameters are defined in those files
(each parameters are described in
http://www.sklogwiki.org/SklogWiki/index.php/TIP4P-Ew_model_of_water):
- r_OH and r_OM [A]
- HOH [deg]
- epsilon [kcal/mol]
- q(O), q(H), and q(M) [e]
However, I could not find any definition of 'sigma [A]' (in other word,
a value of 'sigma [A]') in those files.
So I grep a value of 'sigma [A]' (3.15365) under `dat/leap` directory
but it seems only `dat/leap/parm/opls.info` file defined that value.
That's why I wonder where the definition of 'sigma [A]' of TIP4P-EW (or
TIP4P-2005/TIP4P-D) is located.
I would like to modify 'sigma [A]' parameter as well, without using a
unfamiliar OPLS forcefield.
I may mis-understand the way to use a new water model so could anybody
give me a direction?
Thanks for reading.
Asai.
1. Piana S, Donchev AG, Robustelli P, Shaw DE (2015) Water Dispersion
Interactions Strongly Influence Simulated Structural Properties of
Disordered Protein States. J Phys Chem B 119: 5113–5123.
2.
http://www.sklogwiki.org/SklogWiki/index.php/TIP4P/2005_model_of_water
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Received on Wed Jul 27 2016 - 04:00:02 PDT
