Knowledge Base

Article ID: 308 - Last Modified: April 27, 2011

I'm running an IFD run with a metal-containing system. The metal moves during the calculation. How can I force the metal to stay fixed?

If it is Prime that's moving your metal, you should be able to use the 'Do not refine residues' text box in the Prime Refinement tab ('Omitted residues' in the 'Step 2 Prime induced fit' section in earlier releases) to explicitly exclude the metal from optimization. Click the 'Select' button, then pick your metal residue. If you are working from command line, the keyword is:

RESIDUES_TO_OMIT

e.g,: RESIDUES_TO_OMIT A:241

Please note that the metal may also move in the Protein Preparation step. In order to avoid that, you will have to manually prepare the system, making sure that the prepared receptor has the metal in the desired location, and then turn off the Protein Preparation option in IFD (or remove/comment out the PPREP stage in the .inp file).

Keywords: Induced fit, metal containing system, metal moving

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles