AMBER Archive (2005)

Subject: Re: AMBER: Question about PDB format

From: David A. Case (case_at_scripps.edu)
Date: Sat Nov 19 2005 - 12:47:45 CST

On Sat, Nov 19, 2005, FyD wrote:
> 12345678901234567890123456789012345678901234567890123456789012345678901234567890
>
> 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)...

I'm pretty sure this violates the pdb format: the x-coordinate is supposed
to be in columns 31-38, but you have part of the x-coordinate in column 39;
same for y and z.

>
> 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.

This is correct: now the x-coordinate in stored in columns 31-38.

So, as far as I can see, LEaP is doing the correct thing.

...dac

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