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.