Files::PTS: Difference between revisions

From FFDevel Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
Point file specification.
__NOTOC__ __NOEDITSECTION__
 
Navigation: [[Documentation]] / [[Files]] / [[File Formats]] / [[Files::PTS]]
A point file is an extended xyz file. Coordinates are in Å. Extensions are attached as named sections after coordinate specification.  
----
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.  


{|class="wikitable"
{|class="wikitable"
Line 19: Line 20:
| weight of the point
| weight of the point
|-
|-
| CVS
| RST
| definition of collective variables for geometry restraining. The next line contains number of CVs. Description of each CV then follows.
| definition of restraints for geometry optimization. The next line contains number of restraints. Description of each restraints then follows.
|-
|-
| ESP
| 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).
| 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).
|}
==Restraint types==
Each restraint (RST) has order index, followed by a RST type, and target value of RST. The list of currently supported RSTs is provided in the following table:
{|class="wikitable"
| '''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
|}
|}


Line 61: Line 83:
     -0.00516318      -0.00000389      -0.07031707
     -0.00516318      -0.00000389      -0.07031707
       0.03290468      -0.03371502      -0.03452875
       0.03290468      -0.03371502      -0.03452875
RST
2
1 D  169.9998  5  8 11 13
2 B    1.3456  5 11
</pre>
</pre>

Latest revision as of 11:07, 11 March 2019

Navigation: Documentation / Files / File Formats / Files::PTS

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
RST definition of restraints for geometry optimization. The next line contains number of restraints. Description of each restraints 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).

Restraint types

Each restraint (RST) has order index, followed by a RST type, and target value of RST. The list of currently supported RSTs 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
RST
2
1 D   169.9998  5  8 11 13
2 B     1.3456  5 11
Retrieved from "https://ffdevel.ncbr.muni.cz/wiki/index.php?title=Files::PTS&oldid=78"