[gmx-users] i have a question about multiple chain simulation at the same box

[Justin Lemkul]

On 9/5/18 9:25 AM, milad bagheri wrote:
> I'm going to examine the interaction between the two proteins using
> molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1
> from the rcsb , which has two protein(Complex). I want to create a gap
> between two protein, and then with the same coordinate Put these two
> proteins in a box and run MD 100 nanoseconds, for validation this trick
> compare rmsd x-ray pose and Md pose.
> please help me ...

Separate the coordinates of the two proteins, translate one of them with 
editconf, and concatenate the new coordinates back together.

-Justin

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

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jalemkul at vt.edu | (540) 231-3129
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