Files::PTS

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A PTS file format defines geometry and associated properties. The PTS file is an extended xyz file. All coordinates are in Å. Extensions are attached as named sections after coordinate specification. Order of sections is free. It is possible to put several points into a single file and to form a stream of points. In this case, all sections must be supported by ffdevel.

Section	Description
ENERGY	Energy in kcal/mol is provided on the next line.
GRADIENT	Gradient is provided in kcal/mol/Å in three columns starting from the next line.
HESSIAN	Hessian is provided in kcal/mol/Å^2 as the full square matrix.
WEIGHT	weight of the point
CVS	definition of collective variables for geometry restraining. The next line contains number of CVs. Description of each CV then follows.
ESP	definition of electrostatic potential. The next line contains number of ESP points, followed by ESP points. Each ESP point has x, y, and z coordinate in Å and value of ESP (not yet determined).

Collective variables

Each CV has order index, followed by a CV type, and target value of CV. The list of currently supported CVs is provided in the following table:

Type	Value unit	Description
B	Å	distance between two atoms specified by two atom indexes
A	deg	angle between three atoms specified by three atom indexes
D	deg	dihedral angle between four points specified by four atom indexes

Example

14
extracted from gaussian
 6       0.13230016       0.00000077      -1.95468488
 1       0.76809047       0.88672039      -2.09551250
 1      -0.62227433       0.00000027      -2.75333837
 1       0.76809127      -0.88671834      -2.09551220
 6      -0.51108991       0.00000067      -0.56887531
 1      -1.16736722      -0.88018194      -0.46376311
 1      -1.16736732       0.88018319      -0.46376304
 6       0.51109004       0.00000067       0.56887531
 1       1.16736736      -0.88018195       0.46376311
 1       1.16736747       0.88018319       0.46376303
 6      -0.13230001       0.00000077       1.95468489
 1      -0.76809113      -0.88671834       2.09551220
 1       0.62227447       0.00000027       2.75333837
 1      -0.76809032       0.88672039       2.09551250
ENERGY
 -99324.33757012
GRADIENT
      0.11579154       0.00000710      -0.16491661
     -0.03290464      -0.03371546       0.03452853
      0.00516174      -0.00000388       0.07031637
     -0.03290310       0.03371450       0.03453062
     -0.20334654       0.00000002       0.17824297
      0.03625131       0.05934802      -0.03143532
      0.03625573      -0.05935031      -0.03143510
      0.20334573       0.00000003      -0.17824440
     -0.03625143       0.05934780       0.03143565
     -0.03625584      -0.05935008       0.03143544
     -0.11578914       0.00000710       0.16491851
      0.03290314       0.03371407      -0.03453083
     -0.00516318      -0.00000389      -0.07031707
      0.03290468      -0.03371502      -0.03452875
CVS
2
1 D   169.9998  5  8 11 13
2 B     1.3456  5 11