AMBER Archive (2005)

Subject: Re: AMBER: How can I read parm99.dat file?

From: Myunggi Yi (myunggi_at_csit.fsu.edu)
Date: Fri May 06 2005 - 09:14:04 CDT

Let me ask one more question. I want to make sure.

In the parm file, is "IM" data for Cl-(Chloride ion)?
Cl is for Cl(Cholorine)?

Am I right?

Bill Ross wrote:

>For an unbonded ion, only mass and vdw params need to be defined.
>Apparently both are done for I, and the mass line includes a
>value for polarizability. The main issue with the parameters
>is whether the vdw part is right. Given that there are bond and
>angle parameters, the vdw was presumably set for a covalently
>bonded I rather than I-, so this value would need to be
>overridden with a frcmod entry.
>
>It may not make much difference whether you use Cl- or I- if
>the ions are in water.
>
>Some discussion of radii (see 'IONIC RADIUS'):
>
> http://www.chemguide.co.uk/atoms/properties/atradius.html
>
>And a graph of ionic radii:
>
> http://www.physchem.co.za/Atomic/Periodicity.htm
>
>Bill
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-- 
Best wishes,

Myunggi Yi
==========================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL. 32306

(850) 645-1334
http://www.csit.fsu.edu/~myunggi

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