Hi, I think I have new problems here with CNS. The structure contains a DNA with a abasic dideoxyribose（1p,2p-dideoxyribofuranose-5p-phosphate，3DR）. But the pdb genetated by generated_easy.inp lose the abasic site. I used the .param and .top of 3DR on HIC-Up website. They work when the model is 3DR monomer. As a modified base in the DNA, CNS complained as following: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%% bond energy constant missing. target bond length missing. ATOM1: SEGId="C ", RESId="19 ", NAME="O5' ", CHEMical="O_1 " ATOM2: SEGId="C ", RESId="19 ", NAME="C5' ", CHEMical="C5D "
It seems I should write a '3DR.link' or add 3DR to 'dna-rna.link'. Is that right? How can I do that? best wishes, Hongjun Yu
