Wed Dec 28 11:04:15 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 28 2011 at 11:04:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5948303 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -35.32000 11.62000 ymin,ymax (A): 1.454000 41.16100 zmin,zma (A): -1.611000 58.23800 x,y,z range (A): 46.94000 39.70700 59.84900 scale (grids/A): 0.5948303 object centre (A): -11.85000 21.30750 28.31350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.01276 89.51633 89.70012 assigned negative charge : -287.4003 centred at (gu) : 89.91723 89.69126 89.70894 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4673 nv = 96 ne = 84 npr = 40278 no. pairs analyzed = 40278 no. exposed pairs = 2458 no. arc points = 17476 no. surface atoms = 849 nbur = 1121 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 204 mr = 2479 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1786 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7123609E-10 4.7078369E-10 midg,1,midg; midg,igrid,midg 5.2004330E-09 -3.0364236E-09 1,midg,midg; igrid,midg,midg -1.5125168E-09 2.8874063E-09 gauss-seidel spectral radius is 0.9853216 estimated iterations to convergence 68 setup time was (sec) 0.4800000 now iterating at: 11:04:16 rms-change max change #iterations 8.6802810E-02 15.80023 at 10iterations 7.2461469E-03 1.339651 at 20iterations 6.0094183E-04 0.1050129 at 30iterations 4.9520157E-05 7.6084137E-03 at 40iterations 4.0740224E-06 7.2860718E-04 at 50iterations finished qdiffx linear iterations at : 11:04:19 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.0740224E-06 7.2860718E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 11:04:20 3.463u 0.225s 0:04.52 81.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 28 2011 at 11:04:20 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.784491 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -35.32000 11.62000 ymin,ymax (A): 1.454000 41.16100 zmin,zma (A): -1.611000 58.23800 x,y,z range (A): 46.94000 39.70700 59.84900 scale (grids/A): 1.784491 object centre (A): -11.85000 21.30750 28.31350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.03835 88.54906 89.10036 assigned negative charge : -287.4003 centred at (gu) : 89.75198 89.07391 89.12703 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 50746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17476 grid for indexing accessible points = 1.400000 m= 17369 mr = 34340 m= 2098 mr = 12868 m= 76 mr = 1183 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 0.4400000 number of dielectric boundary points 21891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14342 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5948303 object centre at (A) : -11.85000 21.30750 28.31350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6682800E-02 2.2442333E-02 midg,1,midg; midg,igrid,midg 4.2992854E-03 -1.0759265E-02 1,midg,midg; igrid,midg,midg -3.6996552E-03 -1.7573042E-03 gauss-seidel spectral radius is 0.9983699 estimated iterations to convergence 197 setup time was (sec) 0.7400000 now iterating at: 11:04:21 rms-change max change #iterations 3.122585 187.8427 at 10iterations 1.366309 59.72227 at 20iterations 0.5939396 24.82021 at 30iterations 0.2591278 9.738421 at 40iterations 0.1125195 4.587860 at 50iterations 4.9275413E-02 1.916920 at 60iterations 2.1535352E-02 0.8035278 at 70iterations 9.3827695E-03 0.3744640 at 80iterations 4.0790443E-03 0.1487794 at 90iterations 1.7835274E-03 6.7424655E-02 at 100iterations 7.7581330E-04 3.0151367E-02 at 110iterations 3.3954499E-04 1.3113022E-02 at 120iterations finished qdiffx linear iterations at : 11:04:30 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 3.3954499E-04 1.3113022E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 11:04:31 10.601u 0.254s 0:11.18 97.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 28 2011 at 11:04:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.676736 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -35.32000 11.62000 ymin,ymax (A): 1.454000 41.16100 zmin,zma (A): -1.611000 58.23800 x,y,z range (A): 46.94000 39.70700 59.84900 scale (grids/A): 2.676736 object centre (A): -11.85000 21.30750 28.31350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 90.05754 87.82365 88.65070 assigned negative charge : -287.4003 centred at (gu) : 89.62793 88.61098 88.69070 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 117302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17476 grid for indexing accessible points = 1.400000 m= 57624 mr = 83547 m= 19194 mr = 47025 m= 3561 mr = 15408 m= 315 mr = 2577 m= 9 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1161 time to turn everything in is 1.020000 number of dielectric boundary points 49299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 14702 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.784491 object centre at (A) : -11.85000 21.30750 28.31350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2570648 0.1495173 midg,1,midg; midg,igrid,midg 1.1206041E-02 -0.1512260 1,midg,midg; igrid,midg,midg -6.6134974E-02 -4.5516517E-02 gauss-seidel spectral radius is 0.9991636 estimated iterations to convergence 273 setup time was (sec) 1.380000 now iterating at: 11:04:33 rms-change max change #iterations 7.581936 252.7718 at 10iterations 4.247294 175.6414 at 20iterations 2.369381 55.04000 at 30iterations 1.320767 32.03730 at 40iterations 0.7301568 16.28764 at 50iterations 0.4042173 8.927655 at 60iterations 0.2235509 4.947174 at 70iterations 0.1239036 2.905117 at 80iterations 6.8402089E-02 1.586621 at 90iterations 3.7982322E-02 0.8416624 at 100iterations 2.0939091E-02 0.4445724 at 110iterations 1.1613014E-02 0.2979061 at 120iterations 6.4035840E-03 0.1476536 at 130iterations 3.5508508E-03 8.2338333E-02 at 140iterations 1.9632406E-03 4.2144775E-02 at 150iterations 1.0877317E-03 2.6224136E-02 at 160iterations 6.0018292E-04 1.2464523E-02 at 170iterations 3.3225439E-04 7.8274608E-03 at 180iterations finished qdiffx linear iterations at : 11:04:44 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 3.3225439E-04 7.8274608E-03 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 11:04:44 12.618u 0.291s 0:13.35 96.6% 0+0k 0+0io 0pf+0w