Dear Modellers,

Please explain these problems:

1. What each column in *.D* file, which contains details about the optimization, represents? Also, does this file contains details of optimization of molecular pdf as well as Molecular Dynamics? and how to differentiate between them?

2. Running Modeler gives the following warnings:

Number of templates for coordinate transfer: 3 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 3290 1048 TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF

build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates.

I understand that these atoms are undefined because it doesn't found equivalent atoms (same atom name and equivalent residue) in templates but then those atoms are given coordinates by BUILD_MODEL command, but can you tell me how one can find out which are those 'still' undefined atoms , even which are not covered by 'BUILD_MODEL' command and why this is so? Please explain this a bit.

Please clarify these two doubts, really important they are.

sincerely,

vivek sharma