Protein/Ligand complex amber production question

GROMACS version: 2020.4
GROMACS modification: No, except for ligand definition.

I’m trying to run MD simulation of a protein/ligand complex using amber99sb or amber14sb FF.
I’ve followed Justin Lemkul’s tutorial (many thanks) adjusting it to amber, but I do have a question about the production md.mdp file.

Is this md.mdp file from the tutorial OK for amber FF or in contrary specific for the CHARMM36 ff (used in the tutorial) ?

I’ve noticed this in the md.mdp file :
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no

Should I use" DispCorr = EnerPres" for amber FF or any other entry ?

Is there any other parameter in the md.mdp file that I should modify to best fit for amber FF ?

Many thanks for your feedback

Take care
Xavier

Hi,
I suggest those setting for AMBER force fields

constraints = h-bonds ; bonds involving H are constrained
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
vdw-modifier = Potential-shift-Verlet ; Amber specific
DispCorr = EnerPres ; account for cut-off vdW scheme
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
fourierspacing = 0.125 ; grid spacing for FFT

best regards
Alessandra

2 Likes

Hi,
Many thanks Alessandra for your advices
Regards
Xavier

Hi @alevilla ,
Thanks for your answer, I want to ask you if there are any special modifications I need to make in the minim.mdp, nvt.mdp, and npt.mdp files in the same tutorial to be used with Amber forcefield?

Hi @Marwa_92 ,

The force field specific setting includes type of constraints, time step and non-bonded interactions. The other mdp options are usually force field independent. For amber force field, are the one suggested in the post above.
dt = 0.002 (not for energy minimization)
constraints = h-bonds ; bonds involving H are constrained
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
vdw-modifier = Potential-shift-Verlet ; Amber specific
DispCorr = EnerPres ; account for cut-off vdW scheme
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
fourierspacing = 0.125 ; grid spacing for FF

\Alessandra

Thanks @alevilla so much for your help.
I just want to ask if rlist has to be of the same number as rcoulomb and rvdw i.e. here in case of Amber ff , should it too be set to =1.0 ?

Hi,
you can set rlist = 1.0. In general rlist has to be >= rcoulomb /rvdw .
To know more on when rlist value is used see
https://manual.gromacs.org/current/user-guide/mdp-options.html?highlight=rlist#mdp-rlist
\Alessandra

Thank you so much @alevilla, I really appreciate your help!
I just have one more question regarding fourierspacing, I ran a simulation for an apoprotein using Amber99SB ff and fourierspacing value was set to 0.16, is that a problem? And if I want to run a simulation now with a ligand-protein complex to compare the effect of the ligand should I set it to 0.16 or 0.125?

Hi,
the fourierspacing values affect the accuracy of your calculations. As general rule to evaluate the fourierspacing one can use [cutoff value]/8. A value larger than this will makes the calculation inaccurate.

My suggestion is to use the simulation you ran to have an idea of what is going on in the system, but not for data production (e.i publication). Then I will rerun the simulations with a smaller identical fourierspacing.

Best regards
Alessandra