Hi Wenqing, I would generate the PDB and CIF files for the ligand using the SMILES string and the Grade webserver. Then, I would place the Grade-generated PDB ligand into your protein using Coot and refine the entire complex in Phenix using the newly formed complex and the CIF file from Grade.
Hope that helps, Tomas On Wed, Apr 9, 2025 at 3:21 PM 李文庆 <liwenqing...@126.com> wrote: > > Dear everyone > > I encountered the following problem while analyzing the crystal structure of > a protein-substrate small molecule complex. when I attempted to optimize the > structure of the complex, I input the following four files into > phenix.refine: the amino acid sequence file, the PDB file of the > substrate-containing complex (manually added and saved in coot), the electron > density map file (MTZ format), and the corresponding ligand CIF file (see > Figure 1). However, when I ran the refine program, the following error > message was displayed: "Fatal problems interpreting model file: Number of > atomswith unknown nonbonded energy type symbols: 15 Please editthe model file > to resolve the problems and/or supply a ClFfile with matching restraint > definitions, along withapply_cif modification and apply_cif link > parameterdefinitions if necessary." (see Figure 2). > > Even though the ligand CIF file was provided, this error still occurred. I > have tried multiple methods, such as using the ligand's PDB file and SMILES > string to recreate the ligand's CIF file through phenix > (elBOW), but none of these solutions worked. > > As a newcomer to structural biology, am I missing some crucial information？or > are there other ways to resolve the issue? > > I greatly appreciate your assistance and the time you are taking to help with > the matter. > > > Wenqing LI > Nanjing Agriculture University > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
