Hello Sudakshina-- > I have a ligand pdb and I want to include it in my structure calculations. I > am > not able to understand how to proceed. I tried using the script genligand.py > to > generate the PSF but certain errors were shown. I would like to know exactly > how > to proceed, whether this script will generate parameter and topology files > for my > ligand or I need to prepare these files from PRODRG or any other such server.
Currently, genLingand is only useful for the case of a completely rigid ligand. For flexible ligands PRODRG or another source of .top and .par files is required. > Also should I prepare the ligand PSF separately or do I have to generate a > combined DNA-ligand PSF as the starting structure? Since I am just starting > with > ligand generation in Xplor, an overview of the entire process would be really > appreciated. Thank you for your time. Initially you can choose either separate, or combined PSFs, but in the long run a single PSF is usually most convenient. Please let us know if you have further questions. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
