AMBER Archive (2008)

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

From: Pablo Englebienne (pablo.englebienne_at_mcgill.ca)
Date: Wed Aug 20 2008 - 12:40:11 CDT

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! 

-- 
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

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