Dear all
I am looking to carry out a
pH-REMD calculation involving
a non-standard titratable
residue, which is going to be
the ligand.
I added the ligand to the
titratable_residues.py script
and then recompiled
AmberTools (2022). Then, I
obtained the cpin file for the
newly added ligand. I then
substituted one of the STATENE
flag values to the string
'DELTAGREF', as described
in the manual.
While running the subsequent
step involving reference
energy estimation with findgref.py, I
encountered the following error
in the standard output:
The program will try to find a range of values for DELTAGREF automatically,
as the argument -dgrefrange was not given
AMBER execution #1: running 1000 MD steps for DELTAGREF = 0.000000 kcal/mol
Traceback (most recent call last):
File "/home/sblab/Amber22/amber22/bin/finddgref.py", line 1329, in
<module>
main(opt)
File "/home/sblab/Amber22/amber22/bin/finddgref.py", line 1138, in main
RunAMBER(opt,log,data,0)
File "/home/sblab/Amber22/amber22/bin/finddgref.py", line 451, in RunAMBER
if re.search("Offset", line):
File "/home/sblab/Amber22/amber22/miniconda/lib/python3.9/re.py", line
201, in search
return _compile(pattern, flags).search(string)
TypeError: cannot use a string pattern on a bytes-like object
Could someone please help me
figure out what went wrong and
how to troubleshoot this?
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Received on Sun Aug 11 2024 - 22:00:02 PDT
