Please use an appropriate subject line. On 11/12/19 5:29 AM, shakuntala dhurua wrote:
hello, Here I want to generate arg.pdb to arg.gro by using amber99sb force field . for test i have used 1 residue of arginine but i got Fatal 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). and following is the attach pdb format which i have used for pdb2gmx ,please suggest me to solve this problem
AMBER does not support zwitterionic forms of single amino acids, at least not within GROMACS. There may be a way to create such residues from the AMBER parameter database, but you'll have to look into published works on their force field parametrization to see if such residue definitions exist.
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