Sat Oct 8 23:31:01 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 Sat Oct 8 2011 at 23:31:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: LEU 298 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6506086 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): -28.19800 26.26900 ymin,ymax (A): -15.28800 27.45700 zmin,zma (A): -6.472000 48.24600 x,y,z range (A): 54.46700 42.74500 54.71800 scale (grids/A): 0.6506086 object centre (A): -0.9645004 6.084501 20.88700 number of atom coordinates read : 2452 total number of charged atoms : 2316 net assigned charge : 13.00002 assigned positive charge : 359.6362 centred at (gu) : 90.50271 89.31892 88.92718 assigned negative charge : -346.6370 centred at (gu) : 90.42661 89.38937 88.91197 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7146 nv = 96 ne = 84 npr = 48999 no. pairs analyzed = 48999 no. exposed pairs = 3200 no. arc points = 22610 no. surface atoms = 1081 nbur = 1371 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3781 m= 4 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2232 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8366 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8975675E-08 2.2120034E-08 midg,1,midg; midg,igrid,midg 4.0385640E-08 1.3647076E-08 1,midg,midg; igrid,midg,midg 1.3415753E-08 3.9772026E-08 gauss-seidel spectral radius is 0.9877528 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 23:31:02 rms-change max change #iterations 0.1523234 27.00915 at 10iterations 1.5742192E-02 2.600176 at 20iterations 1.8502068E-03 0.3185883 at 30iterations 3.3159999E-04 6.4163208E-02 at 40iterations 8.9455250E-05 1.8428802E-02 at 50iterations finished qdiffx linear iterations at : 23:31:05 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.9455250E-05 1.8428802E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 23:31:05 3.363u 0.178s 0:03.82 92.4% 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 Sat Oct 8 2011 at 23:31:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: LEU 298 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.951826 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): -28.19800 26.26900 ymin,ymax (A): -15.28800 27.45700 zmin,zma (A): -6.472000 48.24600 x,y,z range (A): 54.46700 42.74500 54.71800 scale (grids/A): 1.951826 object centre (A): -0.9645004 6.084501 20.88700 number of atom coordinates read : 2452 total number of charged atoms : 2316 net assigned charge : 13.00002 assigned positive charge : 359.6362 centred at (gu) : 91.50755 87.95669 86.78117 assigned negative charge : -346.6370 centred at (gu) : 91.27979 88.16788 86.73608 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22610 grid for indexing accessible points = 1.400000 m= 28194 mr = 51769 m= 4714 mr = 20463 m= 367 mr = 2935 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 325 time to turn everything in is 0.3700000 number of dielectric boundary points 34493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18295 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) : 0.6506086 object centre at (A) : -0.9645004 6.084501 20.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0095145E-02 6.6772357E-02 midg,1,midg; midg,igrid,midg 3.6571261E-02 3.5681387E-03 1,midg,midg; igrid,midg,midg 1.9212570E-02 6.1025664E-02 gauss-seidel spectral radius is 0.9986941 estimated iterations to convergence 219 setup time was (sec) 0.5900000 now iterating at: 23:31:06 rms-change max change #iterations 4.203665 170.7624 at 10iterations 1.991425 64.97020 at 20iterations 0.9442804 30.79111 at 30iterations 0.4524619 13.16848 at 40iterations 0.2140089 7.086060 at 50iterations 0.1016136 3.100323 at 60iterations 4.8430022E-02 1.460327 at 70iterations 2.3178991E-02 0.7850332 at 80iterations 1.1081061E-02 0.3416824 at 90iterations 5.3048707E-03 0.1677332 at 100iterations 2.5631525E-03 7.9895020E-02 at 110iterations 1.2507917E-03 3.9993763E-02 at 120iterations finished qdiffx linear iterations at : 23:31:13 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.2507917E-03 3.9993763E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 23:31:13 7.726u 0.200s 0:08.20 96.5% 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 Sat Oct 8 2011 at 23:31:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: LEU 298 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.927739 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): -28.19800 26.26900 ymin,ymax (A): -15.28800 27.45700 zmin,zma (A): -6.472000 48.24600 x,y,z range (A): 54.46700 42.74500 54.71800 scale (grids/A): 2.927739 object centre (A): -0.9645004 6.084501 20.88700 number of atom coordinates read : 2452 total number of charged atoms : 2316 net assigned charge : 13.00002 assigned positive charge : 359.6362 centred at (gu) : 92.26117 86.93484 85.17167 assigned negative charge : -346.6370 centred at (gu) : 91.91968 87.25184 85.10411 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 176959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22610 grid for indexing accessible points = 1.400000 m= 89819 mr = 125996 m= 33730 mr = 72440 m= 8402 mr = 26857 m= 1382 mr = 6222 m= 112 mr = 942 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1119 time to turn everything in is 0.9700000 number of dielectric boundary points 77904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 18527 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) : 1.951826 object centre at (A) : -0.9645004 6.084501 20.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5148314 0.9764917 midg,1,midg; midg,igrid,midg 0.3235544 1.5931375E-02 1,midg,midg; igrid,midg,midg 6.5756135E-02 0.5037480 gauss-seidel spectral radius is 0.9992831 estimated iterations to convergence 295 setup time was (sec) 1.210000 now iterating at: 23:31:15 rms-change max change #iterations 9.926563 354.9152 at 10iterations 5.892933 154.3085 at 20iterations 3.483330 69.67751 at 30iterations 2.050505 40.63771 at 40iterations 1.202323 24.88958 at 50iterations 0.7032806 13.66735 at 60iterations 0.4106531 8.080523 at 70iterations 0.2399050 4.375488 at 80iterations 0.1397312 2.651659 at 90iterations 8.1245013E-02 1.493444 at 100iterations 4.7341183E-02 0.8344536 at 110iterations 2.7556645E-02 0.4923706 at 120iterations 1.6077727E-02 0.2851067 at 130iterations 9.3893129E-03 0.1696711 at 140iterations 5.5027427E-03 0.1008091 at 150iterations 3.2581664E-03 6.6400528E-02 at 160iterations 1.9515734E-03 3.8307190E-02 at 170iterations 1.2038860E-03 2.8366089E-02 at 180iterations finished qdiffx linear iterations at : 23:31:26 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 1.2038860E-03 2.8366089E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 23:31:27 12.628u 0.220s 0:13.55 94.7% 0+0k 0+0io 0pf+0w