Sat Oct 8 20:54:21 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 20:54:21 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 = 2577 !!! 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: ZN4 435 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: 0.6195399 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): -31.23000 17.46800 ymin,ymax (A): -23.92800 22.85500 zmin,zma (A): -12.37500 45.08700 x,y,z range (A): 48.69800 46.78300 57.46200 scale (grids/A): 0.6195399 object centre (A): -6.881000 -0.5365000 16.35600 number of atom coordinates read : 2577 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.51672 89.32081 89.52266 assigned negative charge : -388.8955 centred at (gu) : 88.40381 89.36519 89.41167 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6430 nv = 96 ne = 84 npr = 53300 no. pairs analyzed = 53300 no. exposed pairs = 3001 no. arc points = 21726 no. surface atoms = 1009 nbur = 1568 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3553 m= 0 mr = 42 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.2900000 number of dielectric boundary points 3163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2195 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0882067E-09 9.8058717E-09 midg,1,midg; midg,igrid,midg 7.6646200E-09 7.0301909E-10 1,midg,midg; igrid,midg,midg -5.3821050E-09 7.9621216E-09 gauss-seidel spectral radius is 0.9865026 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 20:54:22 rms-change max change #iterations 0.1252392 19.19265 at 10iterations 1.1396507E-02 1.871607 at 20iterations 1.0864037E-03 0.1682625 at 30iterations 1.0146137E-04 1.4442444E-02 at 40iterations 1.0566901E-05 1.8558502E-03 at 50iterations finished qdiffx linear iterations at : 20:54:24 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.0566901E-05 1.8558502E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 20:54:25 3.143u 0.180s 0:03.65 90.9% 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 20:54:25 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 = 2577 !!! 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: ZN4 435 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: 1.858620 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): -31.23000 17.46800 ymin,ymax (A): -23.92800 22.85500 zmin,zma (A): -12.37500 45.08700 x,y,z range (A): 48.69800 46.78300 57.46200 scale (grids/A): 1.858620 object centre (A): -6.881000 -0.5365000 16.35600 number of atom coordinates read : 2577 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.54965 87.96198 88.56762 assigned negative charge : -388.8955 centred at (gu) : 85.21127 88.09530 88.23486 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 24309 mr = 48611 m= 3498 mr = 17923 m= 171 mr = 2106 m= 0 mr = 51 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 2583 time to turn everything in is 0.4900000 number of dielectric boundary points 29194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19325 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) : 0.6195399 object centre at (A) : -6.881000 -0.5365000 16.35600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7452303E-02 2.9211821E-02 midg,1,midg; midg,igrid,midg 1.1592048E-02 5.9509324E-04 1,midg,midg; igrid,midg,midg -3.2017347E-03 3.7800904E-02 gauss-seidel spectral radius is 0.9985632 estimated iterations to convergence 209 setup time was (sec) 0.7600000 now iterating at: 20:54:26 rms-change max change #iterations 4.006560 165.1756 at 10iterations 1.841944 66.35492 at 20iterations 0.8444998 28.88796 at 30iterations 0.3878342 12.45893 at 40iterations 0.1785718 6.126543 at 50iterations 8.2000270E-02 2.998485 at 60iterations 3.7641454E-02 1.274738 at 70iterations 1.7266100E-02 0.6376495 at 80iterations 7.9473965E-03 0.2620068 at 90iterations 3.6534828E-03 0.1311741 at 100iterations 1.6708280E-03 5.5503845E-02 at 110iterations 7.7089941E-04 2.5933743E-02 at 120iterations finished qdiffx linear iterations at : 20:54:32 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 7.7089941E-04 2.5933743E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 20:54:32 6.909u 0.213s 0:07.42 95.8% 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 20:54:32 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 = 2577 !!! 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: ZN4 435 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: 2.787929 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): -31.23000 17.46800 ymin,ymax (A): -23.92800 22.85500 zmin,zma (A): -12.37500 45.08700 x,y,z range (A): 48.69800 46.78300 57.46200 scale (grids/A): 2.787929 object centre (A): -6.881000 -0.5365000 16.35600 number of atom coordinates read : 2577 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.32438 86.94279 87.85129 assigned negative charge : -388.8955 centred at (gu) : 82.81679 87.14288 87.35214 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 161758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 79738 mr = 117604 m= 27545 mr = 65504 m= 6299 mr = 22143 m= 763 mr = 4653 m= 26 mr = 488 m= 0 mr = 8 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 8739 time to turn everything in is 1.210000 number of dielectric boundary points 65729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19727 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) : 1.858620 object centre at (A) : -6.881000 -0.5365000 16.35600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1217180 0.3655750 midg,1,midg; midg,igrid,midg 0.1403814 -1.2288770E-02 1,midg,midg; igrid,midg,midg -5.3967528E-02 0.5041780 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.500000 now iterating at: 20:54:34 rms-change max change #iterations 9.419116 274.0992 at 10iterations 5.411692 112.6278 at 20iterations 3.090072 61.44658 at 30iterations 1.756695 36.66193 at 40iterations 1.001108 20.09132 at 50iterations 0.5704468 11.01441 at 60iterations 0.3248275 6.315212 at 70iterations 0.1846429 3.398908 at 80iterations 0.1051378 2.048283 at 90iterations 5.9701663E-02 1.147041 at 100iterations 3.3944909E-02 0.6946602 at 110iterations 1.9318076E-02 0.3771235 at 120iterations 1.0986369E-02 0.2016106 at 130iterations 6.2435246E-03 0.1182594 at 140iterations 3.5522536E-03 6.8010330E-02 at 150iterations 2.0213381E-03 3.8689375E-02 at 160iterations 1.1546443E-03 2.2534370E-02 at 170iterations 6.5991213E-04 1.2821198E-02 at 180iterations finished qdiffx linear iterations at : 20:54:44 total time elapsed so far: 10.94000 # loops : 180 mean,max change (kT/e) : 6.5991213E-04 1.2821198E-02 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 20:54:44 11.123u 0.207s 0:11.63 97.3% 0+0k 0+0io 0pf+0w