[AMBER] Zn Bond Length solvatebox

From: Lowe, Ben (Ext) <"Lowe,>
Date: Fri, 4 Mar 2011 10:25:53 +0000


I was wondering if anyone could help me with an issue I've been having with regard to dummy atom VDW radii.

I am trying to parameterise Zn2+ in a protein, I've tried using the procedure shown here: http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm at the bottom of the page it has the steps and files used.

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"

Why is not recognizing that all dummy atoms (DZ atom type --> D1 D2 D3 D4) have 0 radii?

Many Thanks for any help,

Ben Lowe

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Received on Fri Mar 04 2011 - 02:30:02 PST
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