[gmx-users] protein peptide interaction

[Justin Lemkul]

On 12/22/17 9:35 PM, MD wrote:
> Hi Gromacs folks,
> Does it make sense to combine the protein and peptide in one pdb file for
> minimization if I want to study the protein peptide interaction? They will
> belong to two different chains in one pdb file.

That is the *only* way you can study the interaction between two 
proteins. You have to supply a suitable starting configuration of both 
of them, and that requires a single coordinate file.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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