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
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