Dear Yew Mun,
> I'm not sure if this is the right place to ask about the R.E.D
> server, so I'm just going to give it a shot.
You can post your questions to the Amber mailing list or to the
q4md-fft mailing list at
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft as you wish.
> I'm planning to simulate a zinc finger where the zinc ion is
> coordinated to 4 other Cys residues. I plan to calculate the charge
> of the Zn ion since coordination would definitely have changed its
> +2 charge.
If you want to have a +2 charge on the Zn(II) (not that obvious) you
will have to set an intra-molecular charge constraint of +2 on this
Zinc atom otherwise the atomic charges of Zn(II) is likely to be far
lower than +2.
See
http://q4md-forcefieldtools.org/REDDB/projects/F-88/ to compare
charges for Fe(III) with an integer charge value (i.e. +3) vs a
non-integer charge value.
> I know I can rely on the RED server for this, but under the charge
> method (e.g. Resp-A1A), how do I know which one is suitable.?
See
http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
RESP-A1A means HF/6-31G*//HF/6-31G*
do you think HF/6-31G* is suitable for bioinorganic complexes?
See once again: http://q4md-forcefieldtools.org/REDDB/projects/F-88/
&
http://onlinelibrary.wiley.com/doi/10.1002/cplu.201200141/abstract
> Also, while the RED website has a tutorial for metal inorganic
> complexes, is there a step by step guide as well on using the RED
> server for deriving charges of metals in proteins.?
See projects in R.E.DD.B.
I hope this helps.
regards, Francois
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Received on Thu Jan 09 2014 - 12:30:03 PST
