Create a box around the constrained part of the system to attach the ligand

[Alejo1982]

Dear all,

While performing a conformational search of a ligand inside a curved surface (toroidal shape), I observed that the ligand moved away from the constrained part of the system.

Is it possible to create a box around the constrained part of the system to attach the ligand to the surface and understand its conformational preferences inside the constrained system?

For more information, please refer to the attached XYZ file.

Best regardds,
David

crest_rotamers_0_xyz.txt

[pprcht]

Have you tried the --wall cli args? this builds such a potential around the entire system rather than just the constrained part, but it might be sufficient already.

[Alejo1982]

I tried all the possible versions (--wall, --wallxl, and --wallxl) as well as --nci. MDP did not run well with the last option. I am sending you the output files for the --wallxl option, which was the last one I used.

What do you suggest I do?

Files.zip

[pprcht]

What do you suggest I do?

For starts, update the 5 year old program version that does not include the --wall commands...

       ==============================================
       |                                            |
       |                 C R E S T                  |
       |                                            |
       |  Conformer-Rotamer Ensemble Sampling Tool  |
       |          based on the GFN methods          |
       |             P.Pracht, S.Grimme             |
       |          Universitaet Bonn, MCTC           |
       ==============================================
       Version 2.11, Mon 1. Feb 10:36:12 CEST 2021
  Using the xTB program. Compatible with xTB version 6.4.0

[Alejo1982]

I changed the version. Now, the problem that I am facing is an issue with geometry optimization. Therefore, I tried to optimize only the ligand inside the constrained molecule with the option --opt and I got a null hessian (See attached folder). What do you suggest I do?

Files.zip