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> 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>
> 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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- application/octet-stream attachment: LIG.cpin
Received on Mon Aug 12 2024 - 09:00:02 PDT
