Mon Oct 10 19:42:23 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 Mon Oct 10 2011 at 19:42:23 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 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: 0.6587591 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): 6.348000 50.97000 ymin,ymax (A): -26.97600 23.81600 zmin,zma (A): -4.824000 49.21700 x,y,z range (A): 44.62200 50.79200 54.04100 scale (grids/A): 0.6587591 object centre (A): 28.65900 -1.580000 22.19650 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 7.2494149E-06 assigned positive charge : 376.8240 centred at (gu) : 91.33340 91.19685 89.18073 assigned negative charge : -376.8250 centred at (gu) : 91.35405 91.15147 89.11266 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7653 nv = 96 ne = 84 npr = 52632 no. pairs analyzed = 52632 no. exposed pairs = 3520 no. arc points = 24093 no. surface atoms = 1182 nbur = 1409 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4064 m= 5 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5064684E-08 1.0587231E-08 midg,1,midg; midg,igrid,midg -6.5117427E-09 1.0899937E-08 1,midg,midg; igrid,midg,midg 2.9313494E-09 -5.0177928E-09 gauss-seidel spectral radius is 0.9880641 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 19:42:23 rms-change max change #iterations 0.1632371 25.30828 at 10iterations 1.7141830E-02 2.422497 at 20iterations 1.9056948E-03 0.2629852 at 30iterations 2.3488965E-04 3.3840179E-02 at 40iterations 4.3834571E-05 7.2536469E-03 at 50iterations finished qdiffx linear iterations at : 19:42:26 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 4.3834571E-05 7.2536469E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 19:42:27 3.294u 0.178s 0:03.89 88.9% 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 Mon Oct 10 2011 at 19:42:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 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: 1.976277 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): 6.348000 50.97000 ymin,ymax (A): -26.97600 23.81600 zmin,zma (A): -4.824000 49.21700 x,y,z range (A): 44.62200 50.79200 54.04100 scale (grids/A): 1.976277 object centre (A): 28.65900 -1.580000 22.19650 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 7.2494149E-06 assigned positive charge : 376.8240 centred at (gu) : 93.99973 93.59011 87.54182 assigned negative charge : -376.8250 centred at (gu) : 94.06198 93.45411 87.33789 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 30277 mr = 55280 m= 5508 mr = 21850 m= 376 mr = 3370 m= 8 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 37207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19407 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) : 0.6587591 object centre at (A) : 28.65900 -1.580000 22.19650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4161231E-02 -1.9519206E-02 midg,1,midg; midg,igrid,midg 2.7440418E-02 1.3222478E-02 1,midg,midg; igrid,midg,midg 1.1356220E-02 -1.8373571E-02 gauss-seidel spectral radius is 0.9987404 estimated iterations to convergence 223 setup time was (sec) 0.8700000 now iterating at: 19:42:28 rms-change max change #iterations 4.491841 203.3296 at 10iterations 2.147704 66.94674 at 20iterations 1.036608 36.19159 at 30iterations 0.4985921 14.98373 at 40iterations 0.2411945 7.339874 at 50iterations 0.1157299 3.710602 at 60iterations 5.5881727E-02 1.637703 at 70iterations 2.6924944E-02 0.8200846 at 80iterations 1.2990274E-02 0.4180712 at 90iterations 6.2806206E-03 0.2216797 at 100iterations 3.0438164E-03 9.4031215E-02 at 110iterations 1.4654668E-03 4.2587280E-02 at 120iterations finished qdiffx linear iterations at : 19:42:34 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 1.4654668E-03 4.2587280E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 19:42:35 7.627u 0.193s 0:08.15 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 Mon Oct 10 2011 at 19:42:35 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 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: 2.964416 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): 6.348000 50.97000 ymin,ymax (A): -26.97600 23.81600 zmin,zma (A): -4.824000 49.21700 x,y,z range (A): 44.62200 50.79200 54.04100 scale (grids/A): 2.964416 object centre (A): 28.65900 -1.580000 22.19650 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 7.2494149E-06 assigned positive charge : 376.8240 centred at (gu) : 95.99937 95.38504 86.31257 assigned negative charge : -376.8250 centred at (gu) : 96.09299 95.18118 86.00683 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 188884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 95079 mr = 134764 m= 37524 mr = 76470 m= 9921 mr = 29705 m= 1544 mr = 7306 m= 107 mr = 959 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 83824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19632 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) : 1.976277 object centre at (A) : 28.65900 -1.580000 22.19650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2549107 -0.3702195 midg,1,midg; midg,igrid,midg 0.4371546 9.2134438E-02 1,midg,midg; igrid,midg,midg 0.1210093 -0.3317683 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 1.780000 now iterating at: 19:42:37 rms-change max change #iterations 10.63554 436.5544 at 10iterations 6.392888 166.7656 at 20iterations 3.822037 92.76668 at 30iterations 2.269591 52.80441 at 40iterations 1.344029 26.71407 at 50iterations 0.7949693 17.34378 at 60iterations 0.4670441 8.676357 at 70iterations 0.2748736 4.797626 at 80iterations 0.1616572 2.832451 at 90iterations 9.4464675E-02 1.694661 at 100iterations 5.5443592E-02 1.112194 at 110iterations 3.2490745E-02 0.5544224 at 120iterations 1.9037450E-02 0.3349810 at 130iterations 1.1130380E-02 0.1859741 at 140iterations 6.5490226E-03 0.1113434 at 150iterations 3.8519404E-03 6.3572884E-02 at 160iterations 2.2844151E-03 3.9875031E-02 at 170iterations 1.3678711E-03 2.2938728E-02 at 180iterations finished qdiffx linear iterations at : 19:42:48 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 1.3678711E-03 2.2938728E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 19:42:49 13.346u 0.224s 0:13.88 97.6% 0+0k 0+0io 0pf+0w