[phenixbb] Re: Error phenix refine with ligands

Hi Pavel, actually someone already helped me and I managed to get my restraints correctly. Thanks anyway, Miriam Inviato da Outlook per Androidhttps://aka.ms/AAb9ysg ________________________________ From: Pavel Afonine Sent: Tuesday, January 7, 2025 6:13:36 PM To: Miriam Cavinato ; [email protected] Subject: Re: [phenixbb] Error phenix refine with ligands [Non ricevi spesso messaggi di posta elettronica da [email protected]. Per informazioni sull'importanza di questo fatto, visita https://aka.ms/LearnAboutSenderIdentification.] Hi Miriam, could you please send me the model file directly? You mentioned it was attached, but I don't see any attachment. I’ll take care of this as soon as I have the file. Best, Pavel On 1/3/25 06:41, [email protected] wrote:

Hi everyone,

I am trying to refine my model containing a ligand (a thiophene -like molecule with a 7 carbon atom cycle attached). I create restraints with ready set utility or directly with eLBOW, then I use phenix.refine and I get this error: "fatal problems in interpreting model file: number of atoms with unknown nonbonded energy type symbols: 12 Please edit the model file to resolve the problems or/and supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definition if necessary". Another problem is that as soon as I try to open REEL or open any result to check restraints, Phenix crashes... I was wondering if someone has the same issue and can help me figure it out! Thanks in advance

Best regards Miriam _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s