Universal ForceField (UFF)

User discussions
1

Hello everyone.
I have a question regarding the use of the Universal ForceField (UFF). I want to apply UFF to Mxene and use it in GROMACS. I found a converter file named OBGMX. When I use it, I can get the itp and top files for my pdb file containing the whole MXene sheet.
The problem here is that when I use my pdb file, all bonds are available and Mxene structure is obvious, but when I do minimization or even equilibration, bonds disappear when I bring .gro file of the simulation to VMD.

I also checked the length of the bonds on VMD and compared it to that available in my itp file, both are the same but still do not have any bonds after simulation.
I was wondering if you could guide me on how to solve this problem.

2

All visualization programs guess where bonds are based on distances. Maybe the PDB file has CONECT records that can be read to override guesses. A .gro file won’t. The point is, what you see in visualization programs is irrelevant. The topology is definitive in terms of which atoms are bonded and bonds cannot break or form in an MM process.

3

Thank you so much.

4

Hi…Could you send me the webpage address that you get the itp and topology file for mxene ?

6

I downloaded obgmx linux patch from this webpage and then used it. But I think it gives the wrong results. not sure yet.

7

Hi Dear Hossein,

Could you please tell me how you used OBGMX? its a bit confusing and there is no tutorial for that in the website.

Thanks