AMBER Archive (2004)

Subject: AMBER: check unit + saveamberparm

From: Carsten Detering (
Date: Wed Feb 18 2004 - 20:21:58 CST

Hi all,

I am having a nucleic acid (RNA) + ligand (theophylline) + three
Magensium atoms + waters + sodium atoms in xleap. When I check the unit,
everything is ok, no errors and such (not even a warning). However, when
  I want to save the amber parameters, leap tells me that it cannot find
the types for the three Magnesium atoms.
Am I missing something here?
I am using amber7.
Here is the output:

> check complex
Checking 'complex'....
Checking parameters for unit 'complex'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveamberparm complex prmtop inpcrd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<RG 1>.A<Mg38 38> Could not find type: Mg
For atom: .R<RG 1>.A<Mg47 47> Could not find type: Mg
For atom: .R<RG 1>.A<Mg52 52> Could not find type: Mg
Parameter file was not saved.

Thanks for any helpful comments.


Carsten Detering
University of Washington
Department of Chemistry
Box 351700
Seattle, WA 98195-1700
Fon 206.543.5081
Fax 206.685.8665

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