# Protein/Ligand complex amber production question **URL:** \ **Category:** User discussions\ **Tags:** forcefield, mdp-parameters\ **Created:** [December 12, 2020, 7:45pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247 "2020-12-12T19:45:18Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![XavierB](https://avatars.discourse-cdn.com/v4/letter/x/b19c9b/32.png) [@XavierB](https://gromacs.bioexcel.eu/u/XavierB)\ **Post date:** [December 12, 2020, 7:45pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/1 "2020-12-12T19:45:18Z")
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 ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [December 14, 2020, 10:06am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/2 "2020-12-14T10:06:43Z")
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 ---
**Author:** ![XavierB](https://avatars.discourse-cdn.com/v4/letter/x/b19c9b/32.png) [@XavierB](https://gromacs.bioexcel.eu/u/XavierB)\ **Post date:** [December 14, 2020, 1:38pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/3 "2020-12-14T13:38:51Z")
Hi, Many thanks Alessandra for your advices Regards Xavier ---
**Author:** ![Marwa\_92](https://avatars.discourse-cdn.com/v4/letter/m/9fc29f/32.png) [@Marwa\_92](https://gromacs.bioexcel.eu/u/Marwa_92)\ **Post date:** [August 23, 2021, 12:34pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/4 "2021-08-23T12:34:30Z")
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? ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [August 24, 2021, 7:39am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/5 "2021-08-24T07:39:02Z")
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 ---
**Author:** ![Marwa\_92](https://avatars.discourse-cdn.com/v4/letter/m/9fc29f/32.png) [@Marwa\_92](https://gromacs.bioexcel.eu/u/Marwa_92)\ **Post date:** [August 24, 2021, 12:26pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/6 "2021-08-24T12:26:56Z")
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 ? ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [August 25, 2021, 9:34am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/7 "2021-08-25T09:34:07Z")
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](https://manual.gromacs.org/current/user-guide/mdp-options.html?highlight=rlist#mdp-rlist) \Alessandra ---
**Author:** ![Marwa\_92](https://avatars.discourse-cdn.com/v4/letter/m/9fc29f/32.png) [@Marwa\_92](https://gromacs.bioexcel.eu/u/Marwa_92)\ **Post date:** [August 25, 2021, 9:51am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/8 "2021-08-25T09:51:01Z")
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? ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [August 27, 2021, 7:42am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-amber-production-question/1247/9 "2021-08-27T07:42:24Z")
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