Conformational Analysis of a Cyclic Macromolecule

Julien

Hi everyone,
I would like to perform conformational analysis of a cyclic macromolecule , specifically Epothilone-D (structure shown below), before proceeding with DFT calculations.
I'm aware that conformational sampling for large, flexible, and cyclic systems can be quite challenging. I'm looking for advice or suggestions on the best methods and tools to use for this purpose.
Some specific points I'd like to clarify:

• What are the most effective conformational search approaches for cyclic systems (eg, molecular dynamics, Monte Carlo, CREST, etc.)?
  
• Should I start from a force-field–based sampling (MMFF, GAFF, etc.) before moving to DFT optimization?
  
• How to deal with ring-closure constraints to avoid unrealistic geometries during the search?
  
  

Any practical workflow examples or software recommendations would be greatly appreciated.

Thank you in advance for your help!

Best regards,

sobereva

The best way is performing MD based on molecular forcefield (e.g. GAFF or GAFF2) to sample conformational space, and then use conformation search code Molclus (http://www.keinsci.com/research/molclus.html) to carry out the search. The use of Molclus is quite flexible, suggested steps:
(1) Ask Molclus to invoke xtb to preoptimize structures of every specific step of the MD trajectory at GFN-FF or more expensive but more accurate GFN2-xTB level, then use the isostat utility in Molclus to sort the resulting structures according to their energies, taking conformers with lowest energies (e.g. lowest 3 kcal/mol conformers) for next step
(2) Ask Molclus to invoke Gaussian/ORCA to further optimize the prescreened structures of last steps and perform frequency analysis, using e.g. B3LYP-D3(BJ)/6-31G* (for Gaussian) or B97-3c (for ORCA), and meantime invoke ORCA to calculate high-level electronic energies using wB97M-V/def2-QZVP (or the cheaper alternative, wB97M-V/def2-TZVP with gCP), then free energies are obtained. BTW: To make molclus run in this way, you should set itask=3 in settings.ini and provide ORCA template input file of single-point task (template_SP.inp) in current folder.
(3) Finally, use isostat to sort the conformers according to free energies, simply take the lowest one, and/or calculate Boltzmann distributions for every conformer by inputting temperature in isostat.

Tutorials of conformation search using Molclus (written in Chinese but you can easily translate them via Google translator):
http://bbs.keinsci.com/thread-577-1-1.html
http://bbs.keinsci.com/thread-16255-1-1.html

If you have any question about using Molclus please let me know.

Julien

sobereva 发表于 2025-11-1 05:24
The best way is performing MD based on molecular forcefield (e.g. GAFF or GAFF2) to sample conformat ...

Dear Professor,
Thank you very much for your informative and insightful reply.
i'm very aware of Molclus code, because i have using it many times, but i'm not familiar in using Gromacs for this kind of job. Could you please provide additional help using Gromacs (steps) ?  thre are many tutorials in the internet, but most of them are unreliable.

Best regards,

sobereva

Julien 发表于 2025-11-5 01:54
Dear Professor,
Thank you very much for your informative and insightful reply.
i'm very aware of ...

If you are not familiar with GROMACS, I suggest simply using xtb to carry out molecular dynamics at GFN-FF forcefield level, in this case you do not need to prepare topology file, so it is extremely easy. See http://bbs.keinsci.com/thread-16255-1-1.html for example (this tutorial used GFN0-xTB; to use GFN-FF instead, simply replacing "--gfn 0" with "--gfnff" in the xtb running command line. GFN-FF is notably cheaper than GFN0-xTB, while its accuracy in representing relative conformation energies is slightly better than GFN0-xTB).