Hello Nitin,
Try using the following line instead and let me know if it works:
STATENE=0.0,DELTAGREF,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Nitin Kulhar <bo18resch11002.iith.ac.in>
Sent: Monday, August 12, 2024 8:59 AM
To: Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com>
Cc: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] finddgref.py error with manually added titratable ligand
Hi Dr Cruzeiro
PFA the cpin file.
Thanks and regards
Nitin Kulhar
On Mon, Aug 12, 2024 at 9:10 PM Vinicius Cruzeiro <vcruzeiro.architecttherapeutics.com<mailto:vcruzeiro.architecttherapeutics.com>> wrote:
Hello,
Could you please share your CPIN file?
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: @vwcruzeiro
On Aug 11, 2024, at 9:31 PM, Nitin Kulhar via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
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 Mon Aug 12 2024 - 10:30:02 PDT
