ForceBalance force field reader crashed
Posted: Wed Jul 07, 2021 5:48 pm
Dear madam or sir:
I am using ForceBalance with a GROMACS-formatted force field file (.itp). It is crashing upon reading in the atomtype fields and is crashing on each line. I am not sure what is going on, since the format of the fields is the same as a file I had used before. (Furthermore, I assumed, perhaps incorrectly, that the file is parsed based on simple whitespace.) Here is the error for one of the lines:
Traceback (most recent call last):
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance- 1.5.0-py2.7-linux-x86_64.egg/forcebalance/forcefield.py", line 541, in addff_txt
self.Readers[ffname].feed(line)
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance-1.5.0-py2.7-linux-x86_64.egg/forcebalance/gmxio.py", line 430, in feed
self.itype = fdict[self.sec][self.nbtype]
TypeError: list indices must be integers, not NoneType
The force field reader crashed when trying to read the following line:
ALG1 13 26.981540 0.000 A 0.356359487256 2.71960
The entire file is too big for an attachment, so I have attached a representative portion of the .itp that is giving problems (the atom types).
UPDATE: I tried to modify the file, thinking that the force field reader is expecting a certain number of characters in each field. So, I reduced the number of decimal places for the floating point fields, but this did not help. Here is the same error message once again:
Traceback (most recent call last):
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance-1.5.0-py2.7-linux-x86_64.egg/forcebalance/forcefield.py", line 541, in addff_txt
self.Readers[ffname].feed(line)
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance-1.5.0-py2.7-linux-x86_64.egg/forcebalance/gmxio.py", line 430, in feed
self.itype = fdict[self.sec][self.nbtype]
TypeError: list indices must be integers, not NoneType
The force field reader crashed when trying to read the following line:
ALG1 13 26.98 0.0000 A 0.35636 2.71960
I have attached a representative portion of this modified file named ffnonbonded_ond_noifdef_mod_short.itp.txt.
Thank you in advance,
Omar Demerdash
I am using ForceBalance with a GROMACS-formatted force field file (.itp). It is crashing upon reading in the atomtype fields and is crashing on each line. I am not sure what is going on, since the format of the fields is the same as a file I had used before. (Furthermore, I assumed, perhaps incorrectly, that the file is parsed based on simple whitespace.) Here is the error for one of the lines:
Traceback (most recent call last):
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance- 1.5.0-py2.7-linux-x86_64.egg/forcebalance/forcefield.py", line 541, in addff_txt
self.Readers[ffname].feed(line)
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance-1.5.0-py2.7-linux-x86_64.egg/forcebalance/gmxio.py", line 430, in feed
self.itype = fdict[self.sec][self.nbtype]
TypeError: list indices must be integers, not NoneType
The force field reader crashed when trying to read the following line:
ALG1 13 26.981540 0.000 A 0.356359487256 2.71960
The entire file is too big for an attachment, so I have attached a representative portion of the .itp that is giving problems (the atom types).
UPDATE: I tried to modify the file, thinking that the force field reader is expecting a certain number of characters in each field. So, I reduced the number of decimal places for the floating point fields, but this did not help. Here is the same error message once again:
Traceback (most recent call last):
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance-1.5.0-py2.7-linux-x86_64.egg/forcebalance/forcefield.py", line 541, in addff_txt
self.Readers[ffname].feed(line)
File "/home/o0d1/.conda/envs/DevVersion_forcebalance_python2_7/lib/python2.7/site-packages/forcebalance-1.5.0-py2.7-linux-x86_64.egg/forcebalance/gmxio.py", line 430, in feed
self.itype = fdict[self.sec][self.nbtype]
TypeError: list indices must be integers, not NoneType
The force field reader crashed when trying to read the following line:
ALG1 13 26.98 0.0000 A 0.35636 2.71960
I have attached a representative portion of this modified file named ffnonbonded_ond_noifdef_mod_short.itp.txt.
Thank you in advance,
Omar Demerdash