Hi,
I am running MD simulations of a Gold-chelate compound with square planar geometry of Au (III). I parametrized the missing force field parameters for Au and its four neighboring atoms using MCPB and VFFDT properly. The issue is that after the full minimization step (without restraint) in MD simulations, the geometry of Au (III) changes from square planar to tetrahedral which is undesired. Could you please guide me on how to solve the issue?
Thanks
It is a bonded model and Au formed 4 covalent bonds formed with two neighboring Chlorine atoms and two neighboring Nitrogen atoms
If you use bonded model, then geometry may be fixed by setting appropriate dihedral angles
Thank you very much for your comment but I have already assigned the correct dihedral angles and the issue still exists.
Just want to know: How N and Cl and distributed around Au? Do you also restrict 'diagonal' bond angles to 180 degrees ?
Dear Zeynab,
is your MD only for the complex (i.e., < 100 atoms) or for a biomolecule + complex?
If it's the former, you might want to consider switching to a more appropriate method, like the semi-empirical quantum-mechanical GFN2-xTB. Biomolecular forcefields are just not made to simulate transition-metal complexes and the problems/complications you are experiencing are a manifestation of that. Even if you get it working, you should be very careful with the results.
If it's the latter (i.e., complex + biomolecule and >> 100 atoms), GFN-FF might be an option, which is also supported by xTB. It will be much faster but less accurate for the Au complex. However, I am pretty sure it will at least retain the square-planar geometry of your complex without any artificial constraints.
Cheers
Jan
Kolattukudy P. Santo I have attached the pdb, mol2 files of my ligand for your consideration.
Here is the FF parameters defined for Au and its neighboring atoms.
BOND
nb-AU 122.88628 2.08367
n-AU 117.93471 2.07460
cl-AU 128.97563 2.41177
ANGL
nb-AU-n 109.04001 80.93
nb-AU-cl 81.66365 134.30
n-AU-cl 87.44199 134.56
ca-nb-AU 126.92224 119.15
ca-n-AU 121.10192 124.67
c-n-AU 126.32786 114.51
cl-AU-cl 64.31479 90.87
DIHE
o-c-n-AU 3 0.00000 0.00 3.00
nb-AU-n-ca 3 0.00000 0.00 3.00
nb-AU-n-c 3 0.00000 0.00 3.00
n-AU-nb-ca 3 0.00000 0.00 3.00
h4-ca-nb-AU 3 0.00000 0.00 3.00
cl-AU-nb-ca 3 0.00000 0.00 3.00
cl-AU-n-ca 3 0.00000 0.00 3.00
cl-AU-n-c 3 0.00000 0.00 3.00
ca-ca-nb-AU 3 0.00000 0.00 3.00
ca-ca-n-AU 3 0.00000 0.00 3.00
ca-c-n-AU 3 0.00000 0.00 3.00
c-ca-nb-AU 3 0.00000 0.00 3.00
Jan-Michael Mewes Thank you very much for your comment. My system is a complex of Au-ligand and a protein of 1489 amino acid residues and DNA moiety. It quite a big system and I have to run it using your latter suggestion. I have done this using already using QM(DFTB)/MM/MD but it was unsuccessful. I will try it using your approach and update you.
Zeynab Fakhar , I have tried to simulate the PDF file you attached with GFN2 and GFN-FF in water. With both methods, the Au stays planar.
With the forcefield GFN-FF, 100 ps of simulation (timestep 1fs) take only 3 minutes, so I think there you have a chance to include the biomolecule. GFN2 about 10 times slower, so no chance to include the biomolecule here.
I have attached trajectories from the GFN-FF simulation for your convenience (100 fs xyz dumps from 160 000 steps total).
Jan-Michael Mewes Thank you so much for helping me to resolve the issue. Did you use the Amber program for running this simulation? Could you please share your input file with me?
Hello Zeynab
You Au angles :
nb-AU-n 109.04001 80.93
nb-AU-cl 81.66365 134.30
n-AU-cl 87.44199 134.56
cl-AU-cl 64.31479 90.87
These angles dont add up to 360, for the configuration to be plannar.
Kolattukudy P. Santo Thank you very much for your guidance. I modified the Angles parameters as follows but still, I got tetrahedral geometry of Au-ligand:
nb-AU-n 80.93475 80.93
nb-AU-cl 93.98529 93.98
n-AU-cl 94.22774 94.22
cl-AU-cl 90.87238 90.87
ca-nb-AU 125.68697 125.68
ca-n-AU 124.66941 124.67
c-n-AU 114.50690 114.51
Jan-Michael Mewes I am running my simulations through HPC cluster and I don't have xtb installed on the cluster. Could you please suggest an alternative solution for my simulations?
Thanks
Zeynab Fakhar : Ok. Now is it possible for you to represent the two cl atoms by different names, just like you represented n and nb, for Nitrogen? I feel like your angle assignment with cl is ambiguous!
Kolattukudy P. Santo : The cl presentations like n (sp2 N in amide) and nb (inner sp2 N in conj. ring systems) are coming from GAFF atom type presented in Amber FF.
Kolattukudy P. Santo Could you please check the attached pdb file generated using the modified angels? Now the geometry is something between tetrahedral and square planar.
Zeynab Fakhar : They are not plannar. When you define n-Au-cl (or nb-Au-cl) angle, it applies to both cl atoms, so in that case you cannot get a planar geometry as both angles will be set to 90s. When I look at the structure, this is what I see .
Kolattukudy P. Santo I absolutely got your point. I applied the changes as you advised and the problem is solved. Thank you very much!
Zeynab Fakhar : You are welcome! Great to know it is resolved.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Atomic, Molecular and Optical Physics
- Atoms