Re: AMBER: Problems loading pdb file including Mg ions

From: Idan Gabdank <>
Date: Wed, 24 Oct 2007 15:05:46 +0200

Dear Peter,
Thank you very much for your help.
I am using Amber9.

I am trying to load to leap pdb file [1Y26] of adenine riboswitch with
its ligand and Mg ions.
I found the reasons to my mistakes, the problem with angles and bond
parameters was due to the CONNECT section of pdb file I tried to load -
so I deleted all CONNECT entries in the file - which solved this problem.

The problem with addition of heavy atoms was indeed because sugar
phosphate addition - but I don't want them to be added... Actually this
is the ligand (Adenine) and it has to remain without sugar and phosphate
- how can I manage to tell that to LEap? It converts automatically this
ADE to RA3 and adds sugar and phosphate...

The problem of not integral charge is also due to this conversion of
ligand adenine into terminal residue...



Peter Varnai wrote:
> 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,
> Peter
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Received on Sun Oct 28 2007 - 06:07:07 PDT
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