Wenqing You can also send the files to me (offline) and I'll advise.
Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Wed, Apr 9, 2025 at 7:33 AM Tomas Malinauskas < tomas.malinaus...@gmail.com> wrote: > 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/ > ######################################################################## 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/
