Thanks for Alicia and Modeler taker's kind hlep last time. Here come some new questions. Basically I just want to build a homology model complexed with an additional ligand. This time, I created a small molecule(ethane) to test whether the method works. First,In InsightII, I built ethane and optimized using cvff ( the program did not allow me to use charmm22 at that time.) and output it as an RTF file in charmm22 force field.- Second, I did some modification to some of the library files: 1. append part of the content of RTF file to the end of top_allh.lib and top_heav.lib 2. add an entry to restyp.lib, use j as the one letter abbreviation. (142 | ETH | j | ETHL | ethyl )
Third, alignment was modified so that "j' was appended to the end of the target sequence and '-' was used in the relative position of the template sequence. The program worked well with the above changes, but I could not see any ligand shown in the created pdb file! I could see heme was shown as the 513th residue but no ethane was shown as the 514th residue! Here I attached the ali file,wish you can give me some suggestions. Again, I would like to ask whether it is correct for me to just put any ligand at the end of the target sequence in the alignment file? Is it necessary to create the restraint file when some ligands are introduced? If fact, in the above test, I just want to see the ligand are really in the final model, and I do not mind where is it? So, anyone can tell me how to make the ligand appear in the final model?