How to make a manually constructed chain (by PyMOL) collapsed

User discussions
1

I have built a sequence using PyMOL (which cannot be found in RCSB PDB) and I would like to run a simulation of it. However, the chain is so long and stretched that it needs an extremely big box and costs much. I wonder how to make the chain more collapsed before simulation?

2

Hi Liujy,

You can have a look at Protein Folding using the Broker to help you fold the chain into something more compact.

3

Thank you very much!

4

I found another way — use GROMACS to run a simulation without solvate or ions, after which the chain will collapse. Then I can perform a normal simulation.