Open yauz3 opened 2 years ago
Hi again, Does this error: "Could not triangle bounds smooth molecule." affect the results?
Thank you a lot.
@yauz3 Hello, does this error: "Could not triangle bounds smooth molecule." affect the results? because i met the new error: Traceback (most recent call last):
File "/data2/zcq/protac/PROTAC-Model-master/main.py", line 102, in
Hi, have you solved it? I have the same problem: [16:56:05] WARNING: More than one matching pattern found - picking one [16:56:05] Could not triangle bounds smooth molecule. /bin/bash: /root/miniconda2/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Hi, @Krystal0310.
You need to find the SOAP file on the internet. Then, adopt codes, which I already defined in the previous comment.
I hope you can solve it.
Hi. I would like to write something about error I faced : "SOAP-potential file not found". This maybe helps someone.
The codes were:
The outputs: frodock> Name H convention: pdb frodock> Force Field: CHARMM frodock> frodock> Reading receptor PDB frodock> Receptor PDB center: -0.598341 -64.294624 -5.272957 frodock> Receptor accessibility read from receptor PDB frodock> ...occupancy column seems to have ASA values frodock> Creating Accessibility map from receptor PDB... frodock> Accessibility map created from receptor PDB frodock> Weights SOAP 0.700000 Tobi 15.000000 frodock> Reading SOAP-potential file: ../bin/soap.bin frodock> �� SOAP-potential file not found ERROR: ��
Then dock.dat file becomes empty, which breaks the code.
You need to add one line to eliminate the error. 1) go to utils/frodock.py 2) Add line just after frodock_gcc = '%s/bin/frodock_gcc' % FRODOCK (line 37) write : soap='%s/bin/soap.bin' % FRODOCK 3) Go to line frodock execution line (it was 46, but now 47) edit that code like that: os.system(frodock_docking + ' receptor_ASA.pdb target_ASA.pdb -w receptor_W.ccp4 -e receptor_E.ccp4 ' '--th 10 -d receptor_DS.ccp4,target_DS.ccp4 -t E -o dock.dat --around %s -s %s' %(site, soap))
I hope it helps someone.