AMBER Archive (2008)

Subject: Re: AMBER: Using Na+ ions as input to leap? - solved

From: Pablo Englebienne (pablo.englebienne_at_mcgill.ca)
Date: Wed Aug 20 2008 - 14:25:25 CDT

I just solved the issue, so I'll just provide the solution in case
somebody else stumbles with the same stone...

The problem was simply the alignment of the residue names: the residue
name should be right-aligned in columns 18-20
(http://www.wwpdb.org/documentation/format23/sect9.html)

Wrong:
ATOM 465 C4 DG A 22 1.913 4.783 -8.158 1.00
0.31 C
HETATM 466 Na+ Na+ 23 0.100 3.543 -2.734 1.00
0.00 Na+
123456789012345678901234567890
                  ^^^
Right:
ATOM 465 C4 DG A 22 1.913 4.783 -8.158 1.00
0.31 C
HETATM 466 Na+ Na+ 23 0.100 3.543 -2.734 1.00
0.00 Na+
123456789012345678901234567890
                 ^^^

This change makes leap recognize and process the PDB file without any
errors.

I hope it helps! 

-- 
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501    Fax (514) 398-2382

"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein

Pablo Englebienne wrote:
> Hi, I'm trying to use a PDB structure of a DNA G-quadruplex which 
> includes structural Na+ ions as input to leap.
>
> What should I set the atom and residue name to? The relevant portion 
> of my PDB input file is:
>
> [...]
> ATOM    465  C4   DG A  22       1.913   4.783  -8.158  1.00  
> 0.31           C
> TER
> HETATM  466  Na+  Na+   23       0.100   3.543  -2.734  1.00  
> 0.00          Na+
> TER
> HETATM  467  Na+  Na+   24       0.946  -1.231  -2.152  1.00  
> 0.00          Na+
> TER
>
> But leap complains:
>
> [...]
> Unknown residue: Na   number: 22   type: Terminal/last
> ..relaxing end constraints to try for a dbase match
>  -no luck
> (Residue 23: Na, Terminal/last, was not found in name map.)
> Unknown residue: Na   number: 23   type: Terminal/last
> ..relaxing end constraints to try for a dbase match
>  -no luck
> [...]
> Checking Unit.
> FATAL:  Atom .R<Na 23>.A<Na+ 1> does not have a type.
> FATAL:  Atom .R<Na 24>.A<Na+ 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> [...]
>
> I'm using parm99 and Amber8.
>
> Thanks for any pointers!
>

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