Hi, everyone,
How do amber trajout pdb with connectivity records? Are there any solutions?
For my trajectory has a user-defined new residue (like phosphorylation and so on), when I trajout one frames to PDB (no connection records) and furthur QM/MM calculation in Gaussian, the Gaussian software often judge the wrong connection, especially the amino acid with benzene ring (PHE, usually the 1.5 bonding and 2.0 bonding).
I further using Discovery or Sybyl to read the original PDBs from Amber to generate the connection records, but the connectivity records is disruptted around the user-defined new residues (no complete connection records generate).
Are there any solutions to generate the complete connection records from Amber?
Thanks for everyone.
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Received on Mon Nov 02 2015 - 19:00:03 PST
