Zinc Finger Bonded Method

User discussions
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1

GROMACS version: 2020.3
GROMACS modification: No

Hello,

I am trying to simulate a Zinc Finger Protein using a bonded method, where there are bonds between the Zn2+ ion and the coordinating residues, in this case, Cys (SG) and His (NE2). How do I implement this into Gromacs, as with AMBER you would set these options in xleap?

Any help would be greatly appreciated

Dan.

2

Hi,
It depends:

  • if you use only harmonic potential between the Zn and SG/NE2, you can add Zn to the topology of the protein and add under [ bonds ] directive Zn SG and Zn NE2 bonds using bond type 6 (see here for syntax File formats — GROMACS 2021.4 documentation ) Note that bond type 6 is special in the treatment of exclusions (see Molecule definition — GROMACS 2021.4 documentation)
  • if the case above does not apply and/or you have also other interactions (e.i angle/dihedral potential between the Zn and protein), then you have to add manually all the missing interactions in the corresponding directive in the topology file.

I hope it helps
Alessandra

3

Hello Alessandra,

Thank you for the suggestion.

Sorry but I don’t quite understand what is meant by “add Zn to the topology of the protein”
I have done this so far to the topology, is this what was intended?

[ bonds ]
; ai aj funct c0 c1 c2 c3
1417 79 1
1417 145 1
1417 370 1
1417 449 1
1418 572 1
1418 625 1
1418 837 1
1418 911 1
1419 1025 1
1419 1066 1
1419 1296 1
1419 1368 1

4

Hi,
Sorry for the late answer. For example if you choose the first option (bond type 6). ZN atoms should be included in the topology under the protein description. More specifically the ZN atoms has to be added under the [atoms] directive and ZN bonds under the directive [ bonds ]

Below an extract from a topol_protein_zn.itp where an harmonic potential (bond type 6) is defined between Zn and N (protein HIS).

[ moleculetype ]
; Name nrexcl
Protein_chain_A_zn 3

[ atoms ]
…
3246 CC 127 PRO C 3246 0.34 12.011 ; qtot -6.66
3247 OC 127 PRO OT1 3247 -0.67 15.9994 ; qtot -7.33
3248 OC 127 PRO OT2 3248 -0.67 15.9994 ; qtot -8
; add zn after the last protein atoms
3249 ZN 910 ZN2 ZN 3249 2 65.37

[bonds]
…
…
3246 3247 1
3246 3248 1
3249 1043 6 0.207 4000 ; ZN-N 1 0.207 16736
3249 768 6 0.207 4000 ; ZN-N 1 0.207 16736

…

If you choose option 2, then the appropriate function has to choose for the bonds and adding has probably to be done in other directives (e.i. [pairs] [angle] …) according to the potential defined in your force field.

I hope it is more clear
Alessandra

5

Hello,

Thank you for the reply and I am sorry my reply is late. Can I ask what numbers 0.207 and 4000 in columns 4 and 5 mean?

Dan.

6

Hi,
0.207 is the value of b0 (nm) and 4000 is the value of K0 in kJ/(mol nm^2). Note the values were specific for my case.
Table 14 in the link below can help you for the syntax of bond-type 6
https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table
\Alessandra

7

Hello,

Thank you for all your suggestions they have been very helpful.

Dan.