RE: Wrapping multimeric protein issues

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Dec 12 2018 - 18:10:57 CST

Hi Jacob,

#3 looks close to what I would do. Compounding on fragment, not residue, would at least prevent a connected protein subunit from itself containing long bonds when it shouldn't, which is what I'm assuming is happening.

-Josh

On 2018-12-12 16:58:18-07:00 owner-namd-l_at_ks.uiuc.edu wrote:

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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fplugins%2Fpbctools%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cd0701c91319c47877f5b08d6608dae09%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636802558984076273&sdata=5oAeu8SE6xqNiJIZReflTejUCdvBVEamqNb8CKw0ykg%3D&reserved=0> 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<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpost%2Fhow_to_use_pbc_wrap_command_in_vmd_to_re-center_a_multimeric_protein&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cd0701c91319c47877f5b08d6608dae09%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636802558984086282&sdata=EuWTWyxWUHwhwE4Oi2RmPI7oUhoQcN6WhwZ62b7aAI0%3D&reserved=0> 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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