Hello Kate--

Your message was too large, so the mailing list server refused it. 

> I've been trying to generate NMR structures for a four-residue peptide,
> cross-linked at two cysteine residues by a cysteine reactive cross-linker. I
> based the script on the example from the 2017 Methods in Molecular Biology 
> paper
> (see attached), and I'm running Xplor-NIH on my Mac. I've also attached the
> modified *.par and *.top files that take care of the cross-linker.
> 
> I've been having mixed results with the script. Sometimes it runs fine, but 
> other
> times it just stops with the message: 
> /Users/Documents/xplor-nih-2.47/bin/xplor:
> line 629: 31470 Killed: 9               /Users/Documents/xplor-nih-2.47/
> bin.Darwin_12_x86_64/xplor '-py' 'fold_bimane.py'
> 

I think the problem is with inconsistent parameters.

I reworked the attached generation script, including the topology and
parameters now in separate files I named new.top and new.par. There
was a single equilibrium angle value in the parameters which needed to
be slightly reduced to avoid covalent violations.

Once the PSF is generated, you need only the
protocol.initParams(('protein','new.par'))
line for future calculations.

Please let us know if you continue to have problems.

best regards--
Charles

Attachment: test.py
Description: Binary data

Attachment: new.top
Description: Binary data

Attachment: new.par
Description: Binary data

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