Sat Oct 15 15:24:57 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 15 2011 at 15:24:57 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6417884 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): -11.75900 37.10900 ymin,ymax (A): -25.65100 22.54200 zmin,zma (A): -10.38800 45.08200 x,y,z range (A): 48.86800 48.19300 55.47000 scale (grids/A): 0.6417884 object centre (A): 12.67500 -1.554500 17.34700 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 2.140012 assigned positive charge : 412.3937 centred at (gu) : 90.33942 90.38318 91.85213 assigned negative charge : -410.2544 centred at (gu) : 90.09281 90.22000 91.75957 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7315 nv = 96 ne = 84 npr = 56702 no. pairs analyzed = 56702 no. exposed pairs = 3230 no. arc points = 22106 no. surface atoms = 1091 nbur = 1646 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 4179 m= 5 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2196 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1180012E-09 2.1992497E-08 midg,1,midg; midg,igrid,midg -1.7063092E-08 2.5600373E-08 1,midg,midg; igrid,midg,midg -2.7682706E-08 3.6444760E-08 gauss-seidel spectral radius is 0.9874252 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 15:24:58 rms-change max change #iterations 0.1510142 19.42464 at 10iterations 1.5329676E-02 2.243042 at 20iterations 1.6085237E-03 0.2211742 at 30iterations 1.9506068E-04 2.6867867E-02 at 40iterations 3.3885590E-05 4.8713684E-03 at 50iterations finished qdiffx linear iterations at : 15:25:01 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 3.3885590E-05 4.8713684E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 15:25:01 3.874u 0.248s 0:04.42 92.9% 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 15 2011 at 15:25:01 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.925365 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): -11.75900 37.10900 ymin,ymax (A): -25.65100 22.54200 zmin,zma (A): -10.38800 45.08200 x,y,z range (A): 48.86800 48.19300 55.47000 scale (grids/A): 1.925365 object centre (A): 12.67500 -1.554500 17.34700 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 2.140012 assigned positive charge : 412.3937 centred at (gu) : 91.01785 91.14876 95.55572 assigned negative charge : -410.2544 centred at (gu) : 90.27821 90.65979 95.27850 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22106 grid for indexing accessible points = 1.400000 m= 29043 mr = 55949 m= 4614 mr = 21840 m= 297 mr = 2991 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 614 time to turn everything in is 0.4100000 number of dielectric boundary points 32044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20342 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) : 0.6417884 object centre at (A) : 12.67500 -1.554500 17.34700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1512200E-02 1.1952306E-02 midg,1,midg; midg,igrid,midg -1.1959297E-02 2.6813872E-02 1,midg,midg; igrid,midg,midg -9.9614458E-03 5.9634332E-02 gauss-seidel spectral radius is 0.9986700 estimated iterations to convergence 217 setup time was (sec) 0.6800000 now iterating at: 15:25:02 rms-change max change #iterations 4.479957 246.3248 at 10iterations 2.118907 71.71594 at 20iterations 1.003129 31.35658 at 30iterations 0.4768308 15.62038 at 40iterations 0.2250657 7.970723 at 50iterations 0.1070159 3.543383 at 60iterations 5.0765216E-02 1.651337 at 70iterations 2.4028616E-02 0.7487237 at 80iterations 1.1398625E-02 0.3905334 at 90iterations 5.4111164E-03 0.1604624 at 100iterations 2.5685369E-03 8.1068039E-02 at 110iterations 1.2225122E-03 3.7765503E-02 at 120iterations finished qdiffx linear iterations at : 15:25:11 total time elapsed so far: 8.950000 # loops : 120 mean,max change (kT/e) : 1.2225122E-03 3.7765503E-02 energy calculations done at 8.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 15:25:11 9.095u 0.285s 0:09.70 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 15 2011 at 15:25:11 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.888047 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): -11.75900 37.10900 ymin,ymax (A): -25.65100 22.54200 zmin,zma (A): -10.38800 45.08200 x,y,z range (A): 48.86800 48.19300 55.47000 scale (grids/A): 2.888047 object centre (A): 12.67500 -1.554500 17.34700 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 2.140012 assigned positive charge : 412.3937 centred at (gu) : 91.52655 91.72314 98.33357 assigned negative charge : -410.2544 centred at (gu) : 90.41722 90.98967 97.91774 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 182593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22106 grid for indexing accessible points = 1.400000 m= 93999 mr = 135126 m= 34119 mr = 77810 m= 8336 mr = 27846 m= 1296 mr = 6474 m= 79 mr = 868 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 1965 time to turn everything in is 1.090000 number of dielectric boundary points 72271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 20670 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) : 1.925365 object centre at (A) : 12.67500 -1.554500 17.34700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7290835 0.3845349 midg,1,midg; midg,igrid,midg -0.1170849 0.3315801 1,midg,midg; igrid,midg,midg -5.8906827E-02 0.5052405 gauss-seidel spectral radius is 0.9992632 estimated iterations to convergence 291 setup time was (sec) 1.380000 now iterating at: 15:25:13 rms-change max change #iterations 10.38777 385.0803 at 10iterations 6.055061 134.1537 at 20iterations 3.536747 73.57111 at 30iterations 2.052480 41.85904 at 40iterations 1.189234 23.13559 at 50iterations 0.6891766 12.01078 at 60iterations 0.3990178 6.756050 at 70iterations 0.2307541 4.112200 at 80iterations 0.1332141 2.405315 at 90iterations 7.6938093E-02 1.346187 at 100iterations 4.4385236E-02 0.7381816 at 110iterations 2.5595631E-02 0.4703283 at 120iterations 1.4781294E-02 0.2784481 at 130iterations 8.5464045E-03 0.1660004 at 140iterations 4.9464079E-03 8.5597515E-02 at 150iterations 2.8649417E-03 5.7016373E-02 at 160iterations 1.6683937E-03 3.0998230E-02 at 170iterations 9.7713957E-04 1.7478943E-02 at 180iterations finished qdiffx linear iterations at : 15:25:26 total time elapsed so far: 14.81000 # loops : 180 mean,max change (kT/e) : 9.7713957E-04 1.7478943E-02 energy calculations done at 14.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.94000 DelPhi exited at 15:25:27 14.941u 0.305s 0:15.52 98.1% 0+0k 0+0io 0pf+0w