Mon Oct 10 16:05:13 PDT 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 Mon Oct 10 2011 at 16:05:13 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5504275 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): 7.016000 58.63100 ymin,ymax (A): -34.24800 29.88700 zmin,zma (A): -35.35900 29.31800 x,y,z range (A): 51.61500 64.13500 64.67700 scale (grids/A): 0.5504275 object centre (A): 32.82350 -2.180501 -3.020501 number of atom coordinates read : 4310 total number of charged atoms : 4201 net assigned charge : 6.000017 assigned positive charge : 653.7791 centred at (gu) : 89.83978 90.22208 91.46404 assigned negative charge : -647.7823 centred at (gu) : 89.83895 90.26992 91.48006 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8516 nv = 96 ne = 84 npr = 86493 no. pairs analyzed = 86493 no. exposed pairs = 5394 no. arc points = 36898 no. surface atoms = 1808 nbur = 2502 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 362 mr = 4612 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3846 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11353 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4330326E-10 3.7147299E-10 midg,1,midg; midg,igrid,midg 9.3703056E-10 -1.0804824E-10 1,midg,midg; igrid,midg,midg 4.5497961E-10 4.3974768E-10 gauss-seidel spectral radius is 0.9830807 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 16:05:14 rms-change max change #iterations 9.5243223E-02 11.63890 at 10iterations 6.8354756E-03 0.8652153 at 20iterations 7.8039430E-04 0.1622238 at 30iterations 2.2032575E-04 4.5383453E-02 at 40iterations 8.2607883E-05 1.4348984E-02 at 50iterations finished qdiffx linear iterations at : 16:05:18 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 8.2607883E-05 1.4348984E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 16:05:18 4.347u 0.230s 0:05.05 90.4% 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 Mon Oct 10 2011 at 16:05:18 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.651282 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): 7.016000 58.63100 ymin,ymax (A): -34.24800 29.88700 zmin,zma (A): -35.35900 29.31800 x,y,z range (A): 51.61500 64.13500 64.67700 scale (grids/A): 1.651282 object centre (A): 32.82350 -2.180501 -3.020501 number of atom coordinates read : 4310 total number of charged atoms : 4201 net assigned charge : 6.000017 assigned positive charge : 653.7791 centred at (gu) : 89.51777 90.66492 94.39079 assigned negative charge : -647.7823 centred at (gu) : 89.51614 90.80930 94.43971 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 95417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30745 mr = 67254 m= 3335 mr = 21315 m= 98 mr = 1639 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 39379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 32306 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) : 0.5504275 object centre at (A) : 32.82350 -2.180501 -3.020501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9271606E-03 9.3097212E-03 midg,1,midg; midg,igrid,midg 1.8835513E-02 1.5538958E-02 1,midg,midg; igrid,midg,midg 2.5227936E-03 6.8381836E-04 gauss-seidel spectral radius is 0.9983662 estimated iterations to convergence 196 setup time was (sec) 1.060000 now iterating at: 16:05:20 rms-change max change #iterations 4.252022 206.2747 at 10iterations 1.853426 56.35287 at 20iterations 0.8107067 27.69611 at 30iterations 0.3534552 10.60646 at 40iterations 0.1546226 4.815403 at 50iterations 6.7527942E-02 2.035027 at 60iterations 2.9618628E-02 0.8348122 at 70iterations 1.2995132E-02 0.4525146 at 80iterations 5.7218843E-03 0.1982975 at 90iterations 2.5524350E-03 8.4999084E-02 at 100iterations 1.1642362E-03 3.6933899E-02 at 110iterations 5.6066865E-04 1.8135071E-02 at 120iterations finished qdiffx linear iterations at : 16:05:28 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 5.6066865E-04 1.8135071E-02 energy calculations done at 9.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 16:05:29 9.809u 0.301s 0:10.39 97.2% 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 Mon Oct 10 2011 at 16:05:29 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4310 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.476924 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): 7.016000 58.63100 ymin,ymax (A): -34.24800 29.88700 zmin,zma (A): -35.35900 29.31800 x,y,z range (A): 51.61500 64.13500 64.67700 scale (grids/A): 2.476924 object centre (A): 32.82350 -2.180501 -3.020501 number of atom coordinates read : 4310 total number of charged atoms : 4201 net assigned charge : 6.000017 assigned positive charge : 653.7791 centred at (gu) : 89.27625 90.99715 96.58602 assigned negative charge : -647.7823 centred at (gu) : 89.27409 91.21378 96.65955 start vw surface at 0.2200000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 222265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36898 grid for indexing accessible points = 1.400000 m= 105912 mr = 164582 m= 30962 mr = 84510 m= 5251 mr = 23268 m= 437 mr = 3468 m= 13 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 88808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 33574 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) : 1.651282 object centre at (A) : 32.82350 -2.180501 -3.020501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6090125E-02 0.3449002 midg,1,midg; midg,igrid,midg 0.2662863 0.3044945 1,midg,midg; igrid,midg,midg 3.1503547E-02 9.9395476E-03 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 2.460000 now iterating at: 16:05:31 rms-change max change #iterations 10.89857 315.8852 at 10iterations 6.377223 138.6931 at 20iterations 3.714567 80.81097 at 30iterations 2.151406 45.25677 at 40iterations 1.240878 23.40186 at 50iterations 0.7151366 12.95184 at 60iterations 0.4105619 7.559811 at 70iterations 0.2359364 4.247091 at 80iterations 0.1350366 2.495854 at 90iterations 7.7398114E-02 1.558428 at 100iterations 4.4265095E-02 0.7707691 at 110iterations 2.5244845E-02 0.5588322 at 120iterations 1.4449088E-02 0.2491970 at 130iterations 8.2703242E-03 0.1481857 at 140iterations 4.7405786E-03 9.9056244E-02 at 150iterations 2.7296192E-03 4.8236132E-02 at 160iterations 1.5924789E-03 3.0643463E-02 at 170iterations 9.4294350E-04 1.8325806E-02 at 180iterations finished qdiffx linear iterations at : 16:05:45 total time elapsed so far: 15.99000 # loops : 180 mean,max change (kT/e) : 9.4294350E-04 1.8325806E-02 energy calculations done at 15.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.16000 DelPhi exited at 16:05:46 16.164u 0.332s 0:16.77 98.3% 0+0k 0+0io 0pf+0w