On Tue, Oct 27, 2015 at 2:51 PM, Abelak, Kavin <kabelak.rvc.ac.uk> wrote:
> Hi,
>
> First of all thanks for the looking over my files and the advice in
> http://archive.ambermd.org/201510/0095.html.
>
> I ran checkValidity in parmed.py on my prmtop/rst7 files and it came back
> with a missingdisulfide error. It seemed to have found a couple of S atoms
> from Cysteines within 3A of each other. However, I had a look at the
> pre-leap pdb and could not find any pairs of Cys which would allow a <3A
> distance between their S atoms.
>
>
>
>
> Has anyone come across this before? There should not be any disulphide
> bridges in my structure so I’m tempted to ignore it, but nevertheless this
> is bugging me.
>
The only time I've seen this report falsely is in metal-containing
systems, but it's certainly possible that there really *shouldn't* be a
disulfide bond where ParmEd thinks one might be missing. But the distance
code is very simple and hard to mess up. Here is the code for that part of
the check:
https://github.com/ParmEd/ParmEd/blob/v1.0/ParmedTools/checkvalidity.py#L251-L270
It is pretty straightforward, simple code.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 27 2015 - 13:00:04 PDT
