SOAP-potential file not found

[yauz3]

Hi. I would like to write something about error I faced : "SOAP-potential file not found". This maybe helps someone.

The codes were:

../bin/frodock 3hfl_fv_ASA.pdb 3hfl_ly2_ASA.pdb -w 3hfl_fv_W.ccp4 -e 3hfl_fv_E.ccp4 --th 10 -d 3hfl_fv_DS.ccp4,3hfl_ly2_DS.ccp4 -o dock.dat

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.

[yauz3]

Hi again, Does this error: "Could not triangle bounds smooth molecule." affect the results?

Thank you a lot.

[zcq23]

@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 main() File "/data2/zcq/protac/PROTAC-Model-master/main.py", line 91, in main fro.filter_frodock(cpu, lig_locate_num, target_smi, rec_smi) File "/data2/zcq/protac/PROTAC-Model-master/utils/frodock.py", line 126, in filter_frodock pool.map(filtering, para_list) File "/home/zqy/miniconda3/envs/protac6/lib/python2.7/multiprocessing/pool.py", line 253, in map return self.map_async(func, iterable, chunksize).get() File "/home/zqy/miniconda3/envs/protac6/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value IndexError: list index out of range after this error. Thanks a lot.

[Krystal0310]

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)

[yauz3]

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.