Hi 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. 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. Sudakshina Ganguly Department of Biophysics Bose Institute India
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