Sat Oct 8 18:51:49 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 18:51:50 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6299324 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): -31.81600 17.45500 ymin,ymax (A): -22.99600 23.82300 zmin,zma (A): -12.27400 44.24000 x,y,z range (A): 49.27100 46.81900 56.51400 scale (grids/A): 0.6299324 object centre (A): -7.180500 0.4134998 15.98300 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.51431 88.76319 89.94392 assigned negative charge : -387.4045 centred at (gu) : 88.42221 88.81091 89.81581 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6743 nv = 96 ne = 84 npr = 54141 no. pairs analyzed = 54141 no. exposed pairs = 2976 no. arc points = 21355 no. surface atoms = 1005 nbur = 1589 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3826 m= 0 mr = 29 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.3000000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2164 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8339 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0729933E-09 1.5318539E-08 midg,1,midg; midg,igrid,midg 1.1231304E-08 2.0959799E-10 1,midg,midg; igrid,midg,midg -5.3279035E-09 9.0227150E-09 gauss-seidel spectral radius is 0.9869419 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 18:51:50 rms-change max change #iterations 0.1369236 21.08243 at 10iterations 1.3237056E-02 2.062393 at 20iterations 1.2590889E-03 0.1875248 at 30iterations 1.2509023E-04 1.7166138E-02 at 40iterations 1.2287889E-05 1.8272400E-03 at 50iterations finished qdiffx linear iterations at : 18:51:53 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.2287889E-05 1.8272400E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 18:51:53 3.166u 0.162s 0:03.64 91.2% 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 Sat Oct 8 2011 at 18:51:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.889797 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): -31.81600 17.45500 ymin,ymax (A): -22.99600 23.82300 zmin,zma (A): -12.27400 44.24000 x,y,z range (A): 49.27100 46.81900 56.51400 scale (grids/A): 1.889797 object centre (A): -7.180500 0.4134998 15.98300 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.54238 86.28909 89.83119 assigned negative charge : -387.4045 centred at (gu) : 85.26643 86.43248 89.44711 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21355 grid for indexing accessible points = 1.400000 m= 26574 mr = 51324 m= 3963 mr = 20026 m= 179 mr = 2540 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3836 time to turn everything in is 0.5000000 number of dielectric boundary points 29785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19276 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) : 0.6299324 object centre at (A) : -7.180500 0.4134998 15.98300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9662194E-02 2.8180603E-02 midg,1,midg; midg,igrid,midg 1.6351465E-02 1.3298845E-03 1,midg,midg; igrid,midg,midg -2.5144652E-03 3.2221548E-02 gauss-seidel spectral radius is 0.9986084 estimated iterations to convergence 212 setup time was (sec) 0.7600000 now iterating at: 18:51:54 rms-change max change #iterations 4.135366 173.4143 at 10iterations 1.926170 71.53185 at 20iterations 0.8952311 30.25256 at 30iterations 0.4147339 13.67369 at 40iterations 0.1934526 6.791138 at 50iterations 9.0127513E-02 2.923599 at 60iterations 4.1970853E-02 1.434392 at 70iterations 1.9476887E-02 0.7144470 at 80iterations 9.0529080E-03 0.3359795 at 90iterations 4.2246911E-03 0.1438713 at 100iterations 1.9616680E-03 6.4888000E-02 at 110iterations 9.1447815E-04 2.7812958E-02 at 120iterations finished qdiffx linear iterations at : 18:52:00 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 9.1447815E-04 2.7812958E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 18:52:01 7.006u 0.183s 0:07.48 95.9% 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 18:52:01 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.834696 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): -31.81600 17.45500 ymin,ymax (A): -22.99600 23.82300 zmin,zma (A): -12.27400 44.24000 x,y,z range (A): 49.27100 46.81900 56.51400 scale (grids/A): 2.834696 object centre (A): -7.180500 0.4134998 15.98300 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.31339 84.43349 89.74675 assigned negative charge : -387.4045 centred at (gu) : 82.89945 84.64880 89.17057 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 168821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21355 grid for indexing accessible points = 1.400000 m= 86516 mr = 124100 m= 31079 mr = 71777 m= 7108 mr = 25334 m= 835 mr = 5474 m= 34 mr = 512 m= 0 mr = 6 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 13153 time to turn everything in is 1.280000 number of dielectric boundary points 67190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19626 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) : 1.889797 object centre at (A) : -7.180500 0.4134998 15.98300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1157052 0.3286335 midg,1,midg; midg,igrid,midg 0.1897713 -1.2230531E-02 1,midg,midg; igrid,midg,midg 2.8316939E-02 0.3799687 gauss-seidel spectral radius is 0.9992450 estimated iterations to convergence 287 setup time was (sec) 1.560000 now iterating at: 18:52:02 rms-change max change #iterations 9.642747 320.6650 at 10iterations 5.552736 120.0449 at 20iterations 3.185077 65.26256 at 30iterations 1.824900 36.79423 at 40iterations 1.045074 21.87335 at 50iterations 0.5978752 11.81206 at 60iterations 0.3416295 6.077423 at 70iterations 0.1955890 3.635294 at 80iterations 0.1117366 2.214680 at 90iterations 6.3746713E-02 1.213163 at 100iterations 3.6511336E-02 0.7410123 at 110iterations 2.0874707E-02 0.3899174 at 120iterations 1.1931414E-02 0.2273922 at 130iterations 6.8157283E-03 0.1290112 at 140iterations 3.8963063E-03 7.1918488E-02 at 150iterations 2.2377688E-03 4.2262077E-02 at 160iterations 1.2839248E-03 2.5629044E-02 at 170iterations 7.4108416E-04 1.6380310E-02 at 180iterations finished qdiffx linear iterations at : 18:52:12 total time elapsed so far: 10.99000 # loops : 180 mean,max change (kT/e) : 7.4108416E-04 1.6380310E-02 energy calculations done at 10.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 18:52:12 11.182u 0.159s 0:11.61 97.5% 0+0k 0+0io 0pf+0w