AMBER Archive (2005)

Subject: AMBER: Question about PDB format

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Nov 19 2005 - 02:11:23 CST

Dear All,

I have a question about the PDB format recognized by LEaP...

The PDB format is described @
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
And the Cart. coord. follow the following format:
         1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL 1
ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N
ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C

If I generate a PDB structure using the builder in LEaP (H2O), I get:
ATOM 1 O1 HHO 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 H2 HHO 1 1.000 0.000 0.000 1.00 0.00
ATOM 3 H3 HHO 1 -0.334 0.943 0.000 1.00 0.00

Now, I decide to add a fourth digit to this water molecule:
ATOM 1 O1 HHO 1 0.0001 0.0001 0.0001 1.00 0.00
ATOM 2 H2 HHO 1 1.0001 0.0001 0.0001 1.00 0.00
ATOM 3 H3 HHO 1 -0.3341 0.9431 0.0001 1.00 0.00
If, I try to reload it in xLEaP. The format is not anymore recognized (water
becomes linear)...

Now, I shift all the Cart. coord. one character to the left:
ATOM 1 O1 HHO 1 0.0001 0.0001 0.0001 1.00 0.00
ATOM 2 H2 HHO 1 1.0001 0.0001 0.0001 1.00 0.00
ATOM 3 H3 HHO 1 -0.3341 0.9431 0.0001 1.00 0.00
If, I try to reload this last struct in xLEaP, the format is this time
recognized.

I think there is the same 'problem' in VMD, but not in molekel...

Why should I shift all the Cart. coord. to the left to get something that makes
sense when I want to use four digits in LEaP ? For me, this does not follow the
official PDB format anymore (I wonder if this problem was not present in
Amber7)...

Thank you, regards, Francois

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