Dear all
I am simulating a protein-ligand complex. During the course of simulation, the cofactor moves far away from the substrate. I want to add distance restraints between protein backbone and cofactor atoms. I refer the manual and tutorials but did not get the full understanding of how to put distance restraint. Could you please help me to do this? Regards Sadaf
Ricardo J Ferreira
Hi,
I think you system may be poorly equilibrated. Apply a protocol in which you remove restraints sequentially: first keep backbone and cofactor restrained, then only cofactor and then fully unrestrained.
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