Wed Dec 21 14:21:46 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+sph2.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 = amb2.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 21 2011 at 14:21:49 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: 251 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= 5.0000001E-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 : 292.9999 centred at (gu) : 90.02824 89.49586 89.69453 assigned negative charge : -291.0002 centred at (gu) : 89.93359 89.66297 89.70405 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 = 0.1200000 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 = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 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 0.4000000 number of grid points assigned charge 5757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9160269E-10 4.5168538E-10 midg,1,midg; midg,igrid,midg 5.0827693E-09 -2.8998841E-09 1,midg,midg; igrid,midg,midg -1.5147732E-09 2.9039657E-09 gauss-seidel spectral radius is 0.9853216 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 14:21:51 rms-change max change #iterations 9.0791650E-02 17.09764 at 10iterations 7.5372267E-03 1.463650 at 20iterations 6.2495196E-04 0.1131020 at 30iterations 5.1707244E-05 8.2092285E-03 at 40iterations 4.2501451E-06 6.7043304E-04 at 50iterations finished qdiffx linear iterations at : 14:21:55 total time elapsed so far: 4.610000 # loops : 50 mean,max change (kT/e) : 4.2501451E-06 6.7043304E-04 energy calculations done at 4.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 14:22:01 4.798u 0.284s 0:12.49 40.5% 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 21 2011 at 14:22:03 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: 251 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= 5.0000001E-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 : 292.9999 centred at (gu) : 90.08472 88.48758 89.08352 assigned negative charge : -291.0002 centred at (gu) : 89.80095 88.98895 89.11229 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 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 = 0.2200000 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 0.4800000 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 0.6100000 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 2.6185941E-02 2.2011092E-02 midg,1,midg; midg,igrid,midg 3.1076390E-03 -1.0419291E-02 1,midg,midg; igrid,midg,midg -3.4036764E-03 -1.3560697E-03 gauss-seidel spectral radius is 0.9983699 estimated iterations to convergence 197 setup time was (sec) 0.7900000 now iterating at: 14:22:05 rms-change max change #iterations 3.181601 187.8427 at 10iterations 1.390904 59.72229 at 20iterations 0.6052334 24.82022 at 30iterations 0.2639107 10.22219 at 40iterations 0.1146649 4.637611 at 50iterations 5.0178211E-02 1.990326 at 60iterations 2.1931609E-02 0.8610229 at 70iterations 9.5555726E-03 0.3950500 at 80iterations 4.1545313E-03 0.1513264 at 90iterations 1.8157536E-03 6.8692207E-02 at 100iterations 7.8986998E-04 3.0746460E-02 at 110iterations 3.4578165E-04 1.3442039E-02 at 120iterations finished qdiffx linear iterations at : 14:22:15 total time elapsed so far: 11.37000 # loops : 120 mean,max change (kT/e) : 3.4578165E-04 1.3442039E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 14:22:18 11.565u 0.308s 0:15.20 78.0% 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 21 2011 at 14:22:18 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: 251 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= 5.0000001E-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 : 292.9999 centred at (gu) : 90.12708 87.73143 88.62543 assigned negative charge : -291.0002 centred at (gu) : 89.70138 88.48354 88.66858 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 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 = 0.6600000 no. cavity mid-points inaccessible to solvent = 1161 time to turn everything in is 1.140000 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 1.280000 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 0.2500657 0.1426374 midg,1,midg; midg,igrid,midg -7.7231089E-03 -0.1469850 1,midg,midg; igrid,midg,midg -6.2082827E-02 -4.0516261E-02 gauss-seidel spectral radius is 0.9991636 estimated iterations to convergence 273 setup time was (sec) 1.450000 now iterating at: 14:22:21 rms-change max change #iterations 7.709994 266.2034 at 10iterations 4.317047 175.6405 at 20iterations 2.409412 57.65886 at 30iterations 1.342259 32.41016 at 40iterations 0.7417913 17.13134 at 50iterations 0.4107530 9.086823 at 60iterations 0.2271309 5.105560 at 70iterations 0.1258407 2.909735 at 80iterations 6.9493867E-02 1.586989 at 90iterations 3.8579017E-02 0.8582822 at 100iterations 2.1267768E-02 0.4570332 at 110iterations 1.1796799E-02 0.2982066 at 120iterations 6.5034311E-03 0.1498070 at 130iterations 3.6075460E-03 8.4518075E-02 at 140iterations 1.9937975E-03 4.4185638E-02 at 150iterations 1.1045332E-03 2.6510239E-02 at 160iterations 6.0911622E-04 1.2781143E-02 at 170iterations 3.3749460E-04 7.4996948E-03 at 180iterations finished qdiffx linear iterations at : 14:22:38 total time elapsed so far: 18.17000 # loops : 180 mean,max change (kT/e) : 3.3749460E-04 7.4996948E-03 energy calculations done at 18.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.38000 DelPhi exited at 14:22:41 18.379u 0.326s 0:23.17 80.6% 0+0k 0+0io 0pf+0w