Hydrogen vsites with nucleotides (ATP)

User discussions
1

GROMACS version:
GROMACS modification: No

I would very much like to use virtual sites for hydrogens in my protein in order to use a longer (4 fs) simulation time step. However, I would also like to include a bound ATP molecule in the system. Using the most recent (July 2020) GROMACS port of charmm36, pdb2gmx fails with the error “No vsite database NH2 entry for type NN1”, which I have been able to track down to the ATP molecule.

Is it possible to either (1) substitute vsites for hydrogens in the protein molecule(s), but not in ATP, or (2) actually put vsites into the ATP molecule?

Also, if I do figure out how to do option 1, how likely are the remaining hydrogens on the bound ATP molecule to cause problems with a 4 fs time step?

2

Either everything needs to be virtualized or nothing. You can’t extend a time step for an entire system with only some of the problematic degrees of freedom manipulated. You’ll have to write a suitable .vsd entry for the relevant ATP functional groups. Not everything is automatically built in.

3

Thanks! I was able to calculate the necessary vsite parameters with MkVSites, an now everything is working.

4

Sorry to revive an older thread but would you be willing to post / share the vsite parameters you generated for ATP?

5

No problem. The force field is charmm36 ported to gmx format by the MacKerell lab, the July 2020 version (MacKerell Lab). Here are the ATP parameters calculated by mkvsites:

Atomtype (add to file atomtypes.atp):

MNH2_1 0.00000

Bonded parameters (add to file ffbonded.itp):

; ATP vsite constraints
MNH2_1 MNH2_1 2 0.060488
MNH2_1 CN2 2 0.146334
; ATP angle constraints
CN7B HN5 2 0.193823
CN7 HN5 2 0.195592

Non-bonded parameters (add to file ffnonbonded.itp):

; dummy particles in ATP
MNH2_1 0 0.000000 0.00 A 0.0 0.0

Vsite database (add to file merged.vsd):

[ NH2 ]
NN1 CN2 MNH2_1

6

I don’t suppose you might also have some advice for constructing the hdb file? I am running into many obstacles with the addition of ADP/ATP ligands to the force field. Any help is appreciated, and thanks for your time already!