AMBER Archive (2009)

Subject: [AMBER] adding MG2 problem

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Jan 30 2009 - 03:45:58 CST

Dear amber ,

I have tried to generate prmtop and inpcrd files using
a PDB which has MG2 .
it has the error
------------------------------------------------------------------------------
Loading PDB file: ./mg_dec2.pdb
Created a new atom named: MG2 within residue: .R<MG2 41>
  Added missing heavy atom: .R<MG2 41>.A<MG 1>
Created a new atom named: MG2 within residue: .R<MG2 42>
  Added missing heavy atom: .R<MG2 42>.A<MG 1>
Created a new atom named: MG2 within residue: .R<MG2 43>
  Added missing heavy atom: .R<MG2 43>.A<MG 1>
Created a new atom named: MG2 within residue: .R<MG2 44>
  Added missing heavy atom: .R<MG2 44>.A<MG 1>
  total atoms in file: 812
  Leap added 456 missing atoms according to residue templates:
       4 Heavy
       452 H / lone pairs
  The file contained 4 atoms not in residue templates
---------------------------------------------------------------------------------------------
when i gave
saveamberparmtop command
the MG2 error came as
----------------------------------------------------------------------------------------------
FATAL: Atom .R<MG2 41>.A<MG2 2> does not have a type.
FATAL: Atom .R<MG2 42>.A<MG2 2> does not have a type.
FATAL: Atom .R<MG2 43>.A<MG2 2> does not have a type.
FATAL: Atom .R<MG2 44>.A<MG2 2> does not have a type.
Failed to generate parameters
Parameter file was not saved.

---------------------------------------------------------------------------------------------

how to solve this
thanks in advance
balaji
UOM

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