Mon Oct 10 17:06:30 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+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 Mon Oct 10 2011 at 17:06:30 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 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: 0.6091823 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): -33.46400 23.57000 ymin,ymax (A): 38.37800 86.48100 zmin,zma (A): 0.1770000 58.61600 x,y,z range (A): 57.03400 48.10300 58.43900 scale (grids/A): 0.6091823 object centre (A): -4.947001 62.42950 29.39650 number of atom coordinates read : 2803 total number of charged atoms : 2663 net assigned charge : 2.000013 assigned positive charge : 423.8363 centred at (gu) : 91.72832 89.91779 89.20335 assigned negative charge : -421.8371 centred at (gu) : 91.67891 89.93917 89.25407 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6815 nv = 96 ne = 84 npr = 57335 no. pairs analyzed = 57335 no. exposed pairs = 3717 no. arc points = 25414 no. surface atoms = 1268 nbur = 1535 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3545 m= 0 mr = 40 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2650 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4398725E-09 -1.3227270E-09 midg,1,midg; midg,igrid,midg 2.2280320E-09 -4.6838686E-11 1,midg,midg; igrid,midg,midg -1.0178628E-09 5.3908704E-09 gauss-seidel spectral radius is 0.9860685 estimated iterations to convergence 69 setup time was (sec) 0.7000000 now iterating at: 17:06:32 rms-change max change #iterations 0.1210306 18.32963 at 10iterations 1.0712577E-02 1.522098 at 20iterations 9.9352514E-04 0.1551170 at 30iterations 1.4395321E-04 2.6198387E-02 at 40iterations 4.2098236E-05 8.6545944E-03 at 50iterations finished qdiffx linear iterations at : 17:06:38 total time elapsed so far: 6.320000 # loops : 50 mean,max change (kT/e) : 4.2098236E-05 8.6545944E-03 energy calculations done at 6.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.660000 DelPhi exited at 17:06:39 6.668u 0.594s 0:08.99 80.6% 0+0k 0+0io 4pf+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 17:06:39 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 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: 1.827547 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): -33.46400 23.57000 ymin,ymax (A): 38.37800 86.48100 zmin,zma (A): 0.1770000 58.61600 x,y,z range (A): 57.03400 48.10300 58.43900 scale (grids/A): 1.827547 object centre (A): -4.947001 62.42950 29.39650 number of atom coordinates read : 2803 total number of charged atoms : 2663 net assigned charge : 2.000013 assigned positive charge : 423.8363 centred at (gu) : 95.18434 89.75279 87.60936 assigned negative charge : -421.8371 centred at (gu) : 95.03643 89.81696 87.76180 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25414 grid for indexing accessible points = 1.400000 m= 24807 mr = 49959 m= 3420 mr = 17450 m= 160 mr = 1914 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 33093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20849 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) : 0.6091823 object centre at (A) : -4.947001 62.42950 29.39650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7095808E-02 -4.3586124E-02 midg,1,midg; midg,igrid,midg 6.8228929E-03 9.0003936E-03 1,midg,midg; igrid,midg,midg -1.1389208E-02 1.0562575E-02 gauss-seidel spectral radius is 0.9985427 estimated iterations to convergence 208 setup time was (sec) 1.000000 now iterating at: 17:06:41 rms-change max change #iterations 4.123389 190.7325 at 10iterations 1.872050 61.66612 at 20iterations 0.8582655 27.48340 at 30iterations 0.3909627 15.57023 at 40iterations 0.1787854 5.881058 at 50iterations 8.1824213E-02 2.489689 at 60iterations 3.7405606E-02 1.228600 at 70iterations 1.7078022E-02 0.5239391 at 80iterations 7.8358129E-03 0.2554169 at 90iterations 3.5970428E-03 0.1129298 at 100iterations 1.6754646E-03 5.3764343E-02 at 110iterations 7.9839857E-04 2.8643608E-02 at 120iterations finished qdiffx linear iterations at : 17:06:52 total time elapsed so far: 10.93000 # loops : 120 mean,max change (kT/e) : 7.9839857E-04 2.8643608E-02 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 17:06:53 11.125u 0.592s 0:13.86 84.4% 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 17:06:53 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 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: 2.741320 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): -33.46400 23.57000 ymin,ymax (A): 38.37800 86.48100 zmin,zma (A): 0.1770000 58.61600 x,y,z range (A): 57.03400 48.10300 58.43900 scale (grids/A): 2.741320 object centre (A): -4.947001 62.42950 29.39650 number of atom coordinates read : 2803 total number of charged atoms : 2663 net assigned charge : 2.000013 assigned positive charge : 423.8363 centred at (gu) : 97.77618 89.62909 86.41358 assigned negative charge : -421.8371 centred at (gu) : 97.55454 89.72535 86.64275 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 171369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25414 grid for indexing accessible points = 1.400000 m= 82215 mr = 121673 m= 27110 mr = 65400 m= 5751 mr = 20879 m= 687 mr = 4076 m= 33 mr = 385 m= 0 mr = 4 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 74748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 21301 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) : 1.827547 object centre at (A) : -4.947001 62.42950 29.39650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7338586 -0.8970237 midg,1,midg; midg,igrid,midg 2.9132148E-02 0.1376226 1,midg,midg; igrid,midg,midg -7.7237494E-02 0.1048550 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.920000 now iterating at: 17:06:56 rms-change max change #iterations 9.995381 394.9329 at 10iterations 5.859517 128.2352 at 20iterations 3.405174 79.55593 at 30iterations 1.975824 42.52355 at 40iterations 1.144077 27.01269 at 50iterations 0.6585883 13.25230 at 60iterations 0.3788838 8.419380 at 70iterations 0.2175498 4.474110 at 80iterations 0.1244726 2.547895 at 90iterations 7.1425542E-02 1.219465 at 100iterations 4.0839832E-02 0.7390141 at 110iterations 2.3420967E-02 0.4395385 at 120iterations 1.3442114E-02 0.2583885 at 130iterations 7.6810382E-03 0.1446228 at 140iterations 4.4177030E-03 7.8660011E-02 at 150iterations 2.5481523E-03 4.6653748E-02 at 160iterations 1.4816563E-03 2.7060509E-02 at 170iterations 8.7417348E-04 1.8920898E-02 at 180iterations finished qdiffx linear iterations at : 17:07:18 total time elapsed so far: 20.09000 # loops : 180 mean,max change (kT/e) : 8.7417348E-04 1.8920898E-02 energy calculations done at 20.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.25000 DelPhi exited at 17:07:18 20.254u 0.562s 0:25.11 82.8% 0+0k 0+0io 0pf+0w