[AMBER] trajout or mask pdb with connection records (title is wrong, see this one)

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From: windy <chxp_moon.163.com>
Date: Tue, 3 Nov 2015 10:55:53 +0800 (CST)

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 - 19:00:04 PST