Sat Oct 8 19:08:30 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+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 Sat Oct 8 2011 at 19:08:30 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: 0.6129688 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): -32.13100 17.58600 ymin,ymax (A): -24.17800 22.44900 zmin,zma (A): -12.67500 45.40300 x,y,z range (A): 49.71700 46.62700 58.07800 scale (grids/A): 0.6129688 object centre (A): -7.272500 -0.8645000 16.36400 number of atom coordinates read : 2586 total number of charged atoms : 2458 net assigned charge : 4.406007 assigned positive charge : 393.8101 centred at (gu) : 88.59375 89.18314 89.70732 assigned negative charge : -389.4045 centred at (gu) : 88.48550 89.22903 89.58829 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6415 nv = 96 ne = 84 npr = 52916 no. pairs analyzed = 52916 no. exposed pairs = 2985 no. arc points = 21928 no. surface atoms = 1010 nbur = 1576 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3635 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 0.3900000 number of dielectric boundary points 3083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2229 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7963 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8377297E-09 8.7117913E-09 midg,1,midg; midg,igrid,midg 6.4909478E-09 3.9768902E-10 1,midg,midg; igrid,midg,midg -4.1816977E-09 6.3976500E-09 gauss-seidel spectral radius is 0.9862174 estimated iterations to convergence 70 setup time was (sec) 0.7200000 now iterating at: 19:08:31 rms-change max change #iterations 0.1224215 21.10988 at 10iterations 1.0804197E-02 1.556325 at 20iterations 9.8114845E-04 0.1433830 at 30iterations 8.5264910E-05 1.2802124E-02 at 40iterations 7.8967605E-06 1.1978149E-03 at 50iterations finished qdiffx linear iterations at : 19:08:34 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 7.8967605E-06 1.1978149E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 19:08:35 4.544u 0.391s 0:05.20 94.8% 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 19:08:35 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: 1.838906 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): -32.13100 17.58600 ymin,ymax (A): -24.17800 22.44900 zmin,zma (A): -12.67500 45.40300 x,y,z range (A): 49.71700 46.62700 58.07800 scale (grids/A): 1.838906 object centre (A): -7.272500 -0.8645000 16.36400 number of atom coordinates read : 2586 total number of charged atoms : 2458 net assigned charge : 4.406007 assigned positive charge : 393.8101 centred at (gu) : 85.78072 87.54906 89.12128 assigned negative charge : -389.4045 centred at (gu) : 85.45644 87.68677 88.76478 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21928 grid for indexing accessible points = 1.400000 m= 25214 mr = 48787 m= 3827 mr = 19090 m= 180 mr = 2515 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 5498 time to turn everything in is 0.7100000 number of dielectric boundary points 28593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 19243 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) : 0.6129688 object centre at (A) : -7.272500 -0.8645000 16.36400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8285781E-02 2.9929325E-02 midg,1,midg; midg,igrid,midg 1.5007479E-02 1.6674314E-03 1,midg,midg; igrid,midg,midg -5.3197155E-03 3.1633426E-02 gauss-seidel spectral radius is 0.9985358 estimated iterations to convergence 207 setup time was (sec) 1.030000 now iterating at: 19:08:36 rms-change max change #iterations 3.942237 164.5901 at 10iterations 1.785696 68.31803 at 20iterations 0.8187639 25.69039 at 30iterations 0.3729382 12.61752 at 40iterations 0.1704150 6.151436 at 50iterations 7.7613316E-02 2.721762 at 60iterations 3.5509389E-02 1.268143 at 70iterations 1.6112253E-02 0.5171509 at 80iterations 7.3524527E-03 0.2418938 at 90iterations 3.3466783E-03 0.1339836 at 100iterations 1.5323939E-03 5.0741196E-02 at 110iterations 6.9770857E-04 2.1097183E-02 at 120iterations finished qdiffx linear iterations at : 19:08:45 total time elapsed so far: 10.16000 # loops : 120 mean,max change (kT/e) : 6.9770857E-04 2.1097183E-02 energy calculations done at 10.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 19:08:46 10.376u 0.443s 0:11.11 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 Sat Oct 8 2011 at 19:08:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: 2.758359 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): -32.13100 17.58600 ymin,ymax (A): -24.17800 22.44900 zmin,zma (A): -12.67500 45.40300 x,y,z range (A): 49.71700 46.62700 58.07800 scale (grids/A): 2.758359 object centre (A): -7.272500 -0.8645000 16.36400 number of atom coordinates read : 2586 total number of charged atoms : 2458 net assigned charge : 4.406007 assigned positive charge : 393.8101 centred at (gu) : 83.67094 86.32364 88.68185 assigned negative charge : -389.4045 centred at (gu) : 83.18465 86.53005 88.14710 start vw surface at 0.1500000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 161509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21928 grid for indexing accessible points = 1.400000 m= 82030 mr = 118010 m= 29149 mr = 68076 m= 6881 mr = 23728 m= 926 mr = 5467 m= 57 mr = 664 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 17971 time to turn everything in is 1.800000 number of dielectric boundary points 64582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 19661 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) : 1.838906 object centre at (A) : -7.272500 -0.8645000 16.36400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0933884E-02 0.4056728 midg,1,midg; midg,igrid,midg 0.1879459 2.7469378E-02 1,midg,midg; igrid,midg,midg -4.6411783E-02 0.4142561 gauss-seidel spectral radius is 0.9992259 estimated iterations to convergence 284 setup time was (sec) 2.160000 now iterating at: 19:08:49 rms-change max change #iterations 9.294312 263.8164 at 10iterations 5.281881 117.3257 at 20iterations 2.995835 56.30103 at 30iterations 1.699480 31.35592 at 40iterations 0.9627881 18.14451 at 50iterations 0.5461109 10.47818 at 60iterations 0.3088619 5.807199 at 70iterations 0.1752037 3.215950 at 80iterations 9.9221282E-02 1.901148 at 90iterations 5.6156754E-02 1.091331 at 100iterations 3.1772964E-02 0.6200809 at 110iterations 1.7976712E-02 0.3357010 at 120iterations 1.0165473E-02 0.1842599 at 130iterations 5.7715219E-03 0.1098576 at 140iterations 3.2618253E-03 6.9458008E-02 at 150iterations 1.8456877E-03 3.3210754E-02 at 160iterations 1.0459074E-03 1.9677162E-02 at 170iterations 5.9230917E-04 1.1489868E-02 at 180iterations finished qdiffx linear iterations at : 19:09:04 total time elapsed so far: 17.53000 # loops : 180 mean,max change (kT/e) : 5.9230917E-04 1.1489868E-02 energy calculations done at 17.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.74000 DelPhi exited at 19:09:05 17.741u 0.475s 0:18.48 98.5% 0+0k 0+0io 0pf+0w