Dear Ai, Are you trying to make phosphodiester bonds in the main chain? Do your modified nucleotides follow the standard atom names (P, OP1, OP2, ..., O3')? If so, you can just change the group name (_chem_comp.group) to RNA (or DNA). Otherwise you could either change atom names to follow the standard, or make link dictionary cif files (using acedrg -L). The link dictionary would be needed for all combinations that happen in the model, so following the standard could be a better solution. However, it depends on what type of modifications your nucleotides have.
If it's not a phosphodiester bond, the link dictionary cif file will need to be created. Best regards, Keitaro On Mon, 28 Aug 2023 at 17:54, Hsuan-Ai <hsuan-ai.c...@uni-wuerzburg.de> wrote: > > Greeting to all, > > I am struggling to place modified nucleotides into an oligonucleotide strand. > I built the ligand restraint dictionaries both in Acedrg or Elbow; the > generated liogands look fine, but the covalent bond between the ligand and > the modification site cannot be generated, also in vain when following the > Acedrg tutorial (where additional covalent bond restraint was generated). I > also tried to edit the pdb file directly by specifying which atom links to > which. It, nevertheless, did mot work as I imagined. > > How do you usually make ligand link to protein / nucleic acid via covalent > bond? Is there some trick to tell the program the existence of covalent > bonds? Any suggestions are heartily appreciated. Thank you in advanced! > > Best regards, > Ai > > ######################################################################## > > 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/
