AMBER: Problems loading pdb file including Mg ions

From: Idan Gabdank <>
Date: Mon, 22 Oct 2007 17:53:12 +0200

I am trying to load correctly into LEaP pdb file of RNA molecule
including 5 Mg+2 ions.
I start the tleap ( or xleap) by:
>>tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.rna.ff99

I changed the name of Magnesium ions in pdb file to be MG2 instead of
MG, I have added the TER in appropriate places, I have changed the OP1
and OP2 atoms to be O1P and O2P so loadpdb would work without errors -
and actually I succeeded to get rid of the majority of the errors except
addition of heavy atoms and H.
myUnit=loadpdb "~/Desktop/file.pdb"
Loading PDB file: /home/idan/Desktop/file.pdb
  Added missing heavy atom: .R<RA3 89>.A<C1' 11>
  Added missing heavy atom: .R<RA3 89>.A<O4' 10>
  Added missing heavy atom: .R<RA3 89>.A<C2' 29>
  Added missing heavy atom: .R<RA3 89>.A<C4' 8>
  Added missing heavy atom: .R<RA3 89>.A<C3' 27>
  Added missing heavy atom: .R<RA3 89>.A<O2' 31>
  Added missing heavy atom: .R<RA3 89>.A<C5' 5>
  Added missing heavy atom: .R<RA3 89>.A<O3' 33>
  Added missing heavy atom: .R<RA3 89>.A<O5' 4>
  Added missing heavy atom: .R<RA3 89>.A<P 1>
  Added missing heavy atom: .R<RA3 89>.A<O1P 2>
  Added missing heavy atom: .R<RA3 89>.A<O2P 3>
  total atoms in file: 1608
  Leap added 970 missing atoms according to residue templates:
       12 Heavy
       958 H / lone pairs

Three problems I am failing to deal with, when I run
>>check myUnit

ERROR: The unperturbed charge of the unit: -60.691900 is not integral.
WARNING: The unperturbed charge of the unit: -60.691900 is not zero.
Could not find angle parameter: OW - MG - OW
Could not find bond parameter for: MG - OW
Warning: Close contact of 1.781064 angstroms between .R<MG....
As for the problem number 1 - I tried to do "addions", and "addions2"
but I am failing to get zero...
Problem number 2 - I don't know what to do, parm99.dat file is loaded -
so I don't know how to try to solve those messages.
Problem number 3 - I don't really know how critical it is - since I can
not try to run any kind of minimization - before I solve the problems
number 2 and 1.

Thank you in advance for your help.

Idan Gabdank
Department of Computer Science
Ben-Gurion University of the Negev
Beer-Sheva, Israel
phone: +972 8 642 8097
email: gabdank at

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Received on Wed Oct 24 2007 - 06:07:33 PDT
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