# Protein-Protein simulation

**URL:** <https://gromacs.bioexcel.eu/t/protein-protein-simulation/882>\
**Category:** User discussions\
**Created:** [September 29, 2020, 7:42am UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882 "2020-09-29T07:42:26Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Nupur\_Nagar](https://avatars.discourse-cdn.com/v4/letter/n/858c86/32.png) [@Nupur\_Nagar](https://gromacs.bioexcel.eu/u/Nupur_Nagar)\
**Post date:** [September 29, 2020, 7:42am UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882/1 "2020-09-29T07:42:26Z")

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GROMACS version: 2018.8  
GROMACS modification: Yes  
Here post your question.  
…  
Hi,

I want to run an MD simulation for a docked protein-protein complex using the OPLS force field and doubt the process.

1. Since it is a protein-protein complex, can I follow the ‘protein-ligand’ MD tutorial by Prof. Justin Lemkul?
2. The protein used as the ligand is a multiepitope vaccine and is very big. So, how to develop a ligand topology for the protein? Also, which topology builder is good for doing so?

Regards

Nupur Nagar

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 29, 2020, 12:04pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882/2 "2020-09-29T12:04:11Z")

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Generate the entire topology with `pdb2gmx`. You have two proteins, nothing more. The second protein is not a “ligand” in the typical sense, which refers to some arbitrary species that is not covered by the force field. Never generate a protein topology with a general force field.

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**Author:** ![venkatareddy](https://avatars.discourse-cdn.com/v4/letter/v/e95f7d/32.png) [@venkatareddy](https://gromacs.bioexcel.eu/u/venkatareddy)\
**Post date:** [September 30, 2020, 12:15pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882/3 "2020-09-30T12:15:02Z")

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Hi,  
What is best force field to simulate the protein-protein complexes?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 30, 2020, 7:02pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882/4 "2020-09-30T19:02:45Z")

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An honest but unsatisfying answer: there is no answer to this question in a general sense. If you find (by studying the literature) that a certain force field models a specific behavior that is relevant in your system very well, use that one.

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**Author:** ![Nupur\_Nagar](https://avatars.discourse-cdn.com/v4/letter/n/858c86/32.png) [@Nupur\_Nagar](https://gromacs.bioexcel.eu/u/Nupur_Nagar)\
**Post date:** [October 1, 2020, 6:52am UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882/5 "2020-10-01T06:52:17Z")

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Hi

Thank a lot for the suggestion. As per your recommendation, I have changed the force field too.

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**Author:** ![venkatareddy](https://avatars.discourse-cdn.com/v4/letter/v/e95f7d/32.png) [@venkatareddy](https://gromacs.bioexcel.eu/u/venkatareddy)\
**Post date:** [October 1, 2020, 7:10am UTC](https://gromacs.bioexcel.eu/t/protein-protein-simulation/882/6 "2020-10-01T07:10:19Z")

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Hi,  
Thank you very much.  
I have come across this:  
[https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00251](https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00251)  
But it also needs further improvements.