[phenixbb] Charged Ammonium ligand exploding

pramod kumar promarksn at gmail.com
Tue Sep 4 13:10:35 PDT 2018

Dear All,

I have a protein-ligand complex cryo-EM data. The ligand is a primary
amine, which at the neutral pH used during data collection, should be NH3+
(alkyl-amonium). However, during realspace refine and despite having
provided the CIF file (elbow generated alkyl-ammonium form), the molecule
keeps "exploding". Instead, the 'NH2 form' (alkyl-amine) remains stable
during refinement and most of the pdb entries having alkylammonium
molecules have modeled them as the amine form even when they are expected
to be positively charged. Thus, it seems to me that other groups may have
gone through the same difficulties when trying to refine ammonium groups.

We have already tried:
* Ligand build in Lidia and tried prodrg with error (*Unrecognised REFMAC
atom type 'HCH3' in input*)
* Refmac Acedrg (run201 Error in wrapper refmac)

Please help me fix this. I could refine using the amine form, but I know
that the amine form is not right.

Thank you very much, in advance.

Promod Jaykar, Ph.D.
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