Dear Amber Community,
I’m trying to use commands via the ParmEd API in my own python program, but I have three problems:
1) The Change command in the below script returns the wrong result. The output from the script reads:
Changing CHARGE of atom # 1663 (FE) from 3.0 to 3.0000
But if I use the ParmEd interpreter on the same (BioDC.prmtop) topology, I get:
> change CHARGE .FE 3.0
Changing CHARGE of atom # 1663 (FE) from 0.43069999999999997 to 3.0000
2) The outparm command in the below script returns:
Traceback (most recent call last):
File "/data/BioDCTestSet/1AKK/oxidized/pmd.py", line 13, in <module>
outparm('test.prmtop')
File "/usr/local/amber22/lib/python3.9/site-packages/parmed/tools/actions.py", line 144, in __init__
raise TypeError('input_parm expected to be a ParmList or Structure instance')
TypeError: input_parm expected to be a ParmList or Structure instance
What does this mean?
3) I need to change the charge on several atoms. What is an efficient way to do this?
Relevant script:
#!/usr/bin/env python
from parmed.amber import AmberParm
from parmed.tools import change
from parmed.tools import outparm
parm = AmberParm('BioDC.prmtop', 'BioDC.rst7')
action = change(parm, "CHARGE", ".FE", 3.0)
action.execute()
print(str(action))
outparm('test.prmtop')
Thank you in advance for the help!
Best,
Matthew
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Received on Sat Dec 16 2023 - 10:00:02 PST
