AMBER Archive (2003)

Subject: Re: protonate

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 08 2003 - 11:06:21 CDT

On Tue, Apr 08, 2003, S.Swaminathan wrote:
>
>
> i see that the 3rd column (atom name) is shifted
> slightly to the left, when compared to the original
> pdb file. Why is it so ? Can we avoid it ?

Try the "-b" option.

> What happens to the last two columns of the input pdb?
> (they are absent in the protonated output file).

Protonate discards the sequence numbers (if this is what you mean by the
"last two columns"); they would be out of order anyway if new atoms were
to be added. You will have to change the code if you need these.

..dac 

-- 

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