AMBER Archive (2004)

Subject: Re: AMBER: problem with protonate

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 05 2004 - 16:31:12 CDT

On Tue, Oct 05, 2004, Richard Stefl wrote:

> bugfix.39 to protonate (AMBER 7.0) causes that some atoms are assigned
> as "mystery protons" and are removed from the output. In my case:
> OH TYR 22 8.39 5.73 -5.09
> HH TYR 22 8.81 6.31 -5.75
> NH1 ARG 67 0.00 5.10 8.94
> HH11 ARG 67 0.17 5.91 9.50
> HH12 ARG 67 -0.09 4.20 9.37
> NH2 ARG 67 -0.31 4.16 6.93
> HH21 ARG 67 -0.31 4.23 5.91
> HH22 ARG 67 -0.41 3.27 7.37
>
> linux> protonate -p -k -d $AMBERHOME/dat/PROTON_INFO.Brook -i test.pdb -o
> test.prot.pdb
>

It looks like you are using protonate to convert an Amber pdb file back
towards Brookhaven-like nomenclature. I can confirm your problem with
Amber 7. Looks like this was only fixed in going to Amber 8. If the rest
looks OK, you could put the mystery protons (and other atoms) back in the
output by hand (as a workaround).

The protonate program was extensively reworked a couple of years ago, and it's
not easy to see how to simply patch version 7 to fix this problem.

...regards....dac
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