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> 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?
--
Disclaimer:- This footer text is to convey that this email is sent by one
of the users of IITH. So, do not mark it as SPAM.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Cvcruzeiro%40architecttherapeutics.com%7Cb890eee26b3f4a7654e908dcba8796be%7C2443aafdae8c417b8e9f735b633fca8a%7C0%7C0%7C638590338719546733%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=LsTIvdrd1bAP1EgeHIF%2BZWIk9tq3tY91NXP%2B0WNNKuQ%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 12 2024 - 09:00:02 PDT
