charlie clark

Thank you. Are you aware of any method that could be used to stitch the flexible residues into the original receptor structure? I'm willing to do the scripting but am unable to assign the new coordinates to the correct atoms as the pdb outputs for the flexible residues are redundant (e.g. all carbon atoms are called C rather than CA, CG, etc...)

apologies, have just seen that my first question has been answered in https://sourceforge.net/p/smina/discussion/help/thread/cef2d93015/ I still am unsure about my second question, however - is it possible to separate the free energy scores of the ligand from the flexible receptor sidechains interatcting with the receptor?

Hi, I'm running minimization of ligands against a receptor using --minimize and I'm also specifying which sidechains should be flexible with --flexres. As soon as I started using --flexres I noticed the free energy scores improved dramatically but the ligands don't seem to be in much more favourable positions (and in many cases, seem as if they would bind much less favorably). In cases where this happen the flexible sidechains do seem to have much less free energy so I suspect that the free energy...

Hi, I'm running minimization of ligands against a receptor using --minimize and I'm also specifying which sidechains should be flexible with --flexres. As soon as I started using --flexres I noticed the free energy scores improved dramatically but the ligands don't seem to be in much more favourable positions (and in many cases, seem as if they would bind much less favorably). In cases where this happen the flexible sidechains do seem to have much less free energy so I suspect that the free energy...