AMBER Archive (2005)

Subject: RE: AMBER: Question about PDB format

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Nov 19 2005 - 10:55:11 CST

Hi Francois,

> 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)...

My understanding (someone correct me if I am wrong) was that the pdb format
is limited to 3 decimal places and that the spaing between coordinates is to
accomodate large coordinate values rather than allow larger accuracy.

E.g.
ATOM 1 O1 HHO 1 103.000 999.000 0.000 1.00 0.00

Thus I think adding a fourth decimal place actually breaks the format
definition and so it is only fortuitous that Leap and VMD can read it. What
if you convert the pdb to mol2 and use that? Does that support more than 3
decimal places? (I am not sure).

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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