Sophie

Sophie

distrib > Mandriva > 2010.2 > i586 > media > contrib-release > by-pkgid > 3d4feffc09bf53cc7a90c5c66529b5c2 > files > 92

gabedit-2.2.9-1mdv2010.1.i586.rpm

[GEOMS]
numberOfGeometries numberOfLabels
nameLabel1 UnitLabel1 nValue1     /* Example : (Dipole D 3) or (Energy eV 1)*/
nameLabel2 UnitLabel2 nValue2     /* (Dipole D 3) or (Energy eV 1)*/
.....
.....
Value1_1 Value1_2 ....   /* begin geometry number 1 */
Value2_1 Value2_2 ....   /* nValue2 values */
....
....
numberOfAtomsBygeometry1
Symbol1 MMType1 PDBType1 ResiduName1 ResidueNumber1 Charge1 Layer1 X1 Y1 Z1 VX1 VY1 VZ1 /* Ang, Layer = 0, 1, or 2 (HIGHT MEDIUM LOWER), VX1 VY1 VZ1 are optionals */
Symbol2 MMType2 PDBType2 ResiduName2 ResidueNumber2 Charge2 Layer2 X2 Y2 Z2 VX2 VY2 VZ2 
....
....
....
Value1 ....   /* begin geometry number 2 */
Value2 ....
....
....
numberOfAtomsBygeometry1
Symbol1 MMType1 PDBType1 ResiduName1 ResidueNumber1 Charge1 Layer1 X1 Y1 Z1 VX1 VY1 VZ1 /* ResiduNumber = 1,2, ...., X, Y and Z in Ang, Layer = 0, 1, or 2 (HIGHT MEDIUM
LOWER)
Symbol2 MMType2 PDBType2 ResiduName2 ResidueNumber2 Charge2 Layer2 X2 Y2 Z2 VX2 VY2 VZ2 
....
....
....
......
......

[MD]
numberOfGeometries
nAtoms time(fs) TotalEnery(Kcal/mol) Kinetic Potential /* begin geometry number 1 */
Symbol1 X1 Y1 Z1 VX1 VY1 VZ1 Charge1 mmType1 pdbType1 residueName1 residueNumber1 /*Coord in Ang, Velocity in AKMA */
Symbol2 X2 Y2 Z2 VX2 VY2 VZ2 Charge2 mmType2 pdbType2 residueName2
.....
.....
nAtoms time(fs) TotalEnery(Kcal/mol) Kinetic Potential /* begin geometry number 2 */
Symbol1 X1 Y1 Z1 VX1 VY1 VZ1 Charge1 mmType1 pdbType1 residueName1 residueNumber1 /*Coord in Ang, Velocity in AKMA */
Symbol2 X2 Y2 Z2 VX2 VY2 VZ2 Charge2 mmType2 pdbType2 residueName2
.....
.....