Re: [AMBER] Zn Bond Length solvatebox

From: Lowe, Ben (Ext) <"Lowe,>
Date: Fri, 4 Mar 2011 12:58:37 +0000

Thanks dac! That solves my issue.

Ben Lowe

-----Original Message-----
From: case []
Sent: 04 March 2011 12:40
To: AMBER Mailing List
Subject: Re: [AMBER] Zn Bond Length solvatebox

On Fri, Mar 04, 2011, Lowe, Ben (Ext) wrote:

> When I try to solvate the ZNB unit using the command solvateBox ZNB
> TIP3BOX 11.
> It says "(using default radius 1.500000 for D1)" and the same message
> for each of the other dummy atoms (D1, D2, D3, D4).
> This implies to me that it hasn't recognized the VDW radii explicitly
> stated in frcmod.zinc:
> DZ 0.000 0.00
> Zn 3.100 1.0E-6"

The "default radius" referred to in the message above refers to the
"dielectric radius" used for GB or PB calculations. It does not refer to the
Lenneard Jones parameters (aka vdW radii) for that atom. Some developer
should change the message to make that clearer.

Note that you can ignore this message if you are not planning to do continuum
solvent calculations (which would be rather dangerous with a +2 ion like


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