Targeted MD, "Biased atoms" and "Fitted atoms", RMSD

From: 黄姝姮 (
Date: Wed Nov 29 2017 - 07:27:15 CST

Dear namd:

I encountered the following problems when using Targeted MD.

 1) I dont really understand what's the different between "Biased atoms" and "Fitted atoms". The original explanation is as follows:
  "Atoms can be separated into non-overlapping constraint domains by assigning integer values in the beta column of the TMDFile. Forces on the atoms will be calculated for each domain independently of the other domains.Within each domain, the set of atoms used to fit the target structure can be different from the set of atoms that are biased towards the target structure."
  "Biased atoms are those whose occupancy (O) is nonzero in the TMD PDB file. Fitted atoms are those whose altloc field is not ‘ ’ or ‘0’, if present, otherwise all biased atoms are fitted."
Dose it means that the "Fitted atoms" will finally fitted with TMDFile2 howeever "Biased atoms" will not?

 2) I have run some TMD simulation where TMDk are set as "15,20,25,30,35,40,45,50". However the RMSD between final structure and target structure are larger than 2.5. Does this mean that the conformation is not fitted? Do ligands require special settings during TMD simulation?

  Looking forward to your reply.

Shuheng Huang
College of Bioengineering, Chongqing University
Adress: No.174,Shazheng street, Shapingba district, Chongqing, China
Mobile: +86 18623510067

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