I am trying to do a MM-GBSA calculation with Prime. When the protein is entirely frozen, it works fine, but if I specify a flexible region > 0 Å, then subprocesses of the calculation die and I don't get any results. What could the problem be?

This problem has been fixed in Schrödinger Suite 2010. Please update your release, or consider the workaround below.

If your receptor structure does not have a chain name, that may be causing this problem. The workaround is to assign a chain name to your receptor by carrying out the following steps.

1) Include your receptor in the Workspace
2) Go to Edit → Build → Residue Properties
3) Select 'Chain Name' from the Property menu
4) Type in a chain name letter in the box provided and click the 'All' button
5) Try running the MM-GBSA job again.

Keywords: MM-GBSA, receptor, chain name, bug, mmgbsa

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