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TinkerTools / poltype2

Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
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Polytype2 error when running with addhydrogens = True #54

Open seanwangsalad opened 2 months ago

seanwangsalad commented 2 months ago

Dear developers,

I am trying to parameterize a protonated guanidium compound. I fed the program an unprotonated compound and specified: structure=guanidio.mol2 addhydrogens = True

However, when I have the "addhydrogens = True" flag, poltype gets hung and I see this being outputted in the .log:

Traceback (most recent call last): File "/opt/anaconda3/envs/mypoltype2/bin/psi4", line 369, in File "/opt/anaconda3/envs/mypoltype2/bin/psi4", line 369, in Traceback (most recent call last): content = psi4.process_input(content) content = psi4.process_input(content) File "/opt/anaconda3/envs/mypoltype2/bin/psi4", line 369, in ^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 702, in process_input File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 702, in process_input Traceback (most recent call last): File "/opt/anaconda3/envs/mypoltype2/bin/psi4", line 369, in content = psi4.process_input(content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 702, in process_input content = psi4.process_input(content) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 702, in process_input temp = re.sub(memory_string, process_memory_command, temp) temp = re.sub(memory_string, process_memory_command, temp) temp = re.sub(memory_string, process_memory_command, temp) temp = re.sub(memory_string, process_memory_command, temp) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/re/init.py", line 186, in sub ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/re/init.py", line 186, in sub ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/re/init.py", line 186, in sub File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/re/init.py", line 186, in sub return _compile(pattern, flags).sub(repl, string, count) return _compile(pattern, flags).sub(repl, string, count) return _compile(pattern, flags).sub(repl, string, count) return _compile(pattern, flags).sub(repl, string, count) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 258, in process_memory_command File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 258, in process_memory_command ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 258, in process_memory_command ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/inputparser.py", line 258, in process_memory_command mem_in_bytes = set_memory(sig + units, execute=False) mem_in_bytes = set_memory(sig + units, execute=False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ mem_in_bytes = set_memory(sig + units, execute=False) mem_in_bytes = set_memory(sig + units, execute=False) File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/p4util/util.py", line 218, in set_memory ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/p4util/util.py", line 218, in set_memory ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/p4util/util.py", line 218, in set_memory File "/opt/anaconda3/envs/mypoltype2/lib/python3.12/site-packages/psi4/driver/p4util/util.py", line 218, in set_memory raise ValidationError( raise ValidationError( psi4.driver.p4util.exceptions.ValidationError: set_memory(): Requested 0.0 MiB (0.0 MB); minimum 250 MiB (263 MB). Please, sir, I want some more. psi4.driver.p4util.exceptions.ValidationError: set_memory(): Requested 0.0 MiB (0.0 MB); minimum 250 MiB (263 MB). Please, sir, I want some more. raise ValidationError( raise ValidationError( psi4.driver.p4util.exceptions.ValidationError: set_memory(): Requested 0.0 MiB (0.0 MB); minimum 250 MiB (263 MB). Please, sir, I want some more. psi4.driver.p4util.exceptions.ValidationError: set_memory(): Requested 0.0 MiB (0.0 MB); minimum 250 MiB (263 MB). Please, sir, I want some more.