Re: AMBER: Problems loading pdb file including Mg ions

From: Peter Varnai <>
Date: Tue, 23 Oct 2007 11:38:53 +0100 (BST)

Dear Idan,

> 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>

this should simply show that your pdb file did not have coordinates
for the sugar-phosphate of the terminal RA3. is that true?

> Three problems I am failing to deal with, when I run
> > > check myUnit
> are:
> 1.
> =================================
> ERROR: The unperturbed charge of the unit: -60.691900 is not integral.
> WARNING: The unperturbed charge of the unit: -60.691900 is not zero.
> 2.
> =================================
> Could not find angle parameter: OW - MG - OW
> Could not find bond parameter for: MG - OW
> 3.
> =================================
> 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...

can you send us details how you tried this? what ions did you try to
add? a simple 'addIons myUnit K+ 0' should work.

the fact that your charge is not integral is not normal. as
non-terminal residues have a -1 charge, you seem to have only a 3'
terminal with -0.69 but not the 5' terminal with -0.31.

> 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.

maybe there are no TER cards before and after MG? Otherwise leap would
not look for bond/angle between MG and OW.

> 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.

i think this is ok.

you are not saying which version of AMBER you are using that would be
helpful in the future; also if you still have problems you could send
the full leap input script it may point to other possible problems.

good luck,
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Received on Wed Oct 24 2007 - 06:07:43 PDT
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