Protein docking with PyRosetta Error!

[Anonymous]

Hi, I’m new PyRosetta user. I’m trying to dock 2 protein by usig D100_Docking.py script. I started with relax these two protein and then combinded into the same file separated by TER line. I aim to generate 1000 decoy first, but ,after run the script, it’s always terminated by below error

ERROR: NAN occurred in H-bonding calculations!
ERROR:: Exit from: src/core/scoring/hbonds/hbonds_geom.cc line: 1187

The script can completely generate decoys, but I never reach to 1000 decoy because this error. For example, after I run the script and I got 45 decoys, the next decoy was terminated by this error.

What happened and how to fix it?

Thanks,

[Anonymous]

It is a know problem. Right now we don’t have a fix for it but only a workaround: what you can do is just detect such situation (catch exception) and discard this decoy. Another approach would be to run protocol multiple times until you have 1k decoys.

Best,

Sergey.

[Anonymous]

Thank you for your answer, Sergey

[Anonymous]

I don’t know exactly approach. I just ignore such exception, however, It worked !. It can run until 1000 decoy. Thanks again, Sergey.

This is my script, now , it work.

while (jd.job_complete == False):
try:
pose.assign(starting_p_centroid)
print “initial perturbation”
perturb.apply(pose)
dock_prot.apply(pose)
print “outputting decoy…”
to_fullatom.apply(pose)
jd.output_decoy(pose)

except RuntimeError :
print “ERROR:NAN occurred in H-bonding calculations!”

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