Hi,
I working on Molecular Dynamics simulation of DNA. I want to study the 5'phosphate attached to thymine 16 number residue in my pdb file. I added these 5' Phosphate attached thymine in dna.rtp file in amber14sb.ff force field. I got the the error in the step
gmx pdb2gmx -f 29mer-de_2.pdb -ignh
Error- There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb).
Thank you in advance
Amnah Alalmaie
Hi Amol
have you solved the problem?
I am having the same problem
Do you have any suggestions?
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