[phenixbb] Charged Ammonium ligand exploding

Pavel Afonine pafonine at lbl.gov
Tue Sep 4 14:51:05 PDT 2018

Hi Pramod,

please send us model before and after refinement and the map. We will 
investigate once we have file and then suggest a solution to you.


On 9/5/18 04:10, pramod kumar wrote:
> 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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