AMBER Archive (2004)

Subject: re: AMBER: check unit + saveamberparm

From: S. Frank Yan (SYan_at_gnf.org)
Date: Fri Feb 20 2004 - 18:17:41 CST

You want to prepare a PREP file for the magnesium ion, and load it into
LEaP before saving the topology file. A sample PREP file can be:

0

Magnesium Ion
MG
MG XYZ 0
CHANGE OMIT DU ALL
0.00
1 DUMM DU M 0.0000 0.0000 0.0000 0.000
2 DUMM DU M 1.0000 0.0000 0.0000 0.000
3 DUMM DU M 1.0000 1.0000 0.0000 0.000
4 MG MG M 2.0000 2.0000 2.0000 2.000

DONE
STOP

Frank

-----Original Message-----
From: Carsten Detering [mailto:detering_at_u.washington.edu]
Sent: Wed 2/18/2004 6:21 PM
To: amber_at_scripps.edu
Cc:
Subject: AMBER: check unit + saveamberparm
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 

-- 
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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