Wrapping multimeric protein issues

From: Jacob Usadi (jusadi_at_uchicago.edu)
Date: Wed Dec 12 2018 - 17:51:55 CST

Hello all,

I have a rather long simulation of a protein with many subunits in solvent.
I wrapped everything during simulation, and now I wish to change things
such that the protein subunits do not jump around across PBC boundaries and
such that bonds do not stretch. How do I achieve this goal?

I have tried a few different methods and have made some progress, but still
have issues. Here is what I've done so far:

1. I did basic wrapping and unwrapping with pbctools, and the system almost
always exploded into a ball of broken bonds.

2. I referred to the PCBTools manual page
<https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/> and started using
the -compound command. I've tinkered with *compound *parameter with pbc
wrap. This helped avoid the broken bond explosion, but the different
subunits still jump across boundaries.

3. Finally, I searched old listhost responses and found a few similar
circumstances. I found this response
which suggested sequential wrap commands, one to center the protein such
that all chains avoid the PBC boundary, and a second to wrap it nicely.
This response results in this sort of command structure:
pbc wrap -center com -centersel "protein and chain A" -compound residue -all
pbc wrap -center com -centersel "protein" -compound residue -all

I found it quite difficult to avoid the PBC boundaries, so a small number
of frames always contained PBC-related jumps. Further, this method
introduced a few cases of bond stretching within residues.

- - - - -

Do you have any additional suggestions to try? Are there questions I should
be asking to understand why I am having these issues?

Thank you very much for your time and guidance,
Jacob Usadi

Jacob Usadi
University of Chicago '19
Mathematics / Computational and Applied Mathematics BS

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