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<p style="margin-top:0;margin-bottom:0">Hi!</p>
<p style="margin-top:0;margin-bottom:0"> I'm trying to do unrestrained refinement of a small molecule in phenix. I have done this many years ago, but it seems whatever I try, phenix.refine now complains about missing nonbonded energy type for all atoms.</p>
<p style="margin-top:0;margin-bottom:0"> The pdb file I supply has the following format (just one line)</p>
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HETATM 33 C81 UNK 1 3.117 14.425 18.765 1.00 1.45 C </span><br>
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<p style="margin-top:0;margin-bottom:0"> <br>
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<p style="margin-top:0;margin-bottom:0">I tried unchecking all references to geometry restraints in the GUI, setting wc and wu to 0<br>
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<p style="margin-top:0;margin-bottom:0"> I also started from a default .eff file and set all references to restraints to either True of False (depending what they said).</p>
<p style="margin-top:0;margin-bottom:0"> I also tried the line from the phenix.refine documentation:</p>
<p style="margin-top:0;margin-bottom:0"><span>phenix.refine ../cif_in/mkt_a.ent ../data/181119/proc/137C3/XDS_17000.HKL strategy=individual_sites wc=0 refinement.input.symmetry_safety_check=warning refinement.input.xray_data.r_free_flags.generate=True</span></p>
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<p style="margin-top:0;margin-bottom:0"> I'm using phenix v 1.14-3260 from an sbgrid environment.</p>
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<p style="margin-top:0;margin-bottom:0"> Any pointers welcome.</p>
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<p style="margin-top:0;margin-bottom:0">Cheers,</p>
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<p style="margin-top:0;margin-bottom:0">Jens<br>
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