# Quantum dot surface and protein interaction

**URL:** <https://gromacs.bioexcel.eu/t/quantum-dot-surface-and-protein-interaction/1385>\
**Category:** User discussions\
**Created:** [January 5, 2021, 6:27am UTC](https://gromacs.bioexcel.eu/t/quantum-dot-surface-and-protein-interaction/1385 "2021-01-05T06:27:08Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sarcoma](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/sarcoma/32/578_2.png) [@sarcoma](https://gromacs.bioexcel.eu/u/sarcoma)\
**Post date:** [January 5, 2021, 6:27am UTC](https://gromacs.bioexcel.eu/t/quantum-dot-surface-and-protein-interaction/1385/1 "2021-01-05T06:27:08Z")

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GROMACS version:5.1.2  
GROMACS modification: Yes  
Here post your question  
hello ,  
gday.! i wish to study interaction between CdTe quantum dot (decorated with ligand) surface and protein(ubq) interactions in gromacs . How do i generate a forcefield for the CdTe surface?  
For now, i have generated ligand[topolgen perl script] and protein topologies using oplsaa forcefield.  
Also, i am beginning my work with computation and was looking for a way to build the spherical quantum dot and ligand decorations. i could find CHARMM GUI but it has limited nos of templates.

thanks in advance

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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:** [January 5, 2021, 3:54pm UTC](https://gromacs.bioexcel.eu/t/quantum-dot-surface-and-protein-interaction/1385/2 "2021-01-05T15:54:09Z")

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> [@sarcoma](#):
>
> How do i generate a forcefield for the CdTe surface?

With extraordinary difficulty.

Biomolecular force fields like OPLS-AA are not particularly well suited to simulating such bizarre species, and the parametrization methodology is unlikely to easily yield parameters for something like this. I’m not even sure it can accurately be done with a pairwise-additive force field.

> [@sarcoma](#):
>
> For now, i have generated ligand[topolgen perl script]

This script is extremely crude and you should do extensive validation of any topology it generates before trusting it for your simulations. It’s really just intended to provide a reasonable skeleton of a topology that can be further refined. It makes a **TON** of assumptions, not all of which are smart.