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
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VIVEK SHARMA
HBG BI