AMBER Archive (2008)

Subject: AMBER: 3fe-4s cluster parameter file generation

From: moitrayee_at_mbu.iisc.ernet.in
Date: Mon Sep 15 2008 - 01:35:39 CDT

Dear Amber Users,

I have generated the prep and frcmod files for [3fe-4s]+1 cluster. But when i am
trying to generate the topology and parameter files using Leap the following
error occurs:-
 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: FE - FE
Could not find bond parameter for: FE - FE
Building angle parameters.
Could not find angle parameter: FE - FE - FE
Could not find angle parameter: S - FE - FE
Could not find angle parameter: S - S - FE
Could not find angle parameter: S - S - S
Could not find angle parameter: S - S - S
Building proper torsion parameters.
 ** No torsion terms for S-FE-FE-FE
 ** No torsion terms for S-S-FE-FE
 ** No torsion terms for S-S-S-FE
 ** No torsion terms for S-S-S-S
Building improper torsion parameters.
old PREP-specified impropers:
 total 4411 improper torsions applied
 0 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
        Quit
But the parameters that are being asked are not involved in the structure's
connectivity at all. There is no Fe-Fe bond at all in the above-mentioned
cluster. Please tell me a way out of this? What can be done to generate the
required topology file.

Sincere Regards,
Moitrayee Bhatacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore-560012
India 

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