Mon Oct 10 17:14:03 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 Mon Oct 10 2011 at 17:14:03 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2874 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5668699 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): -30.70800 32.09300 ymin,ymax (A): -24.96600 24.76500 zmin,zma (A): -8.972000 37.86600 x,y,z range (A): 62.80100 49.73100 46.83800 scale (grids/A): 0.5668699 object centre (A): 0.6925011 -0.1005001 14.44700 number of atom coordinates read : 2874 total number of charged atoms : 2733 net assigned charge : -0.9859747 assigned positive charge : 436.3431 centred at (gu) : 90.70986 90.01617 89.62061 assigned negative charge : -437.3301 centred at (gu) : 90.66059 89.85873 89.49142 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5927 nv = 96 ne = 84 npr = 57878 no. pairs analyzed = 57878 no. exposed pairs = 3794 no. arc points = 26431 no. surface atoms = 1277 nbur = 1597 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 266 mr = 2984 m= 0 mr = 6 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2200000 number of dielectric boundary points 3203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2718 ## 341 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1398083E-09 1.4903847E-09 midg,1,midg; midg,igrid,midg -2.3477724E-09 2.0212629E-09 1,midg,midg; igrid,midg,midg -6.8940942E-10 6.5510364E-10 gauss-seidel spectral radius is 0.9839375 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 17:14:04 rms-change max change #iterations 8.8422455E-02 14.42546 at 10iterations 6.4385473E-03 1.188019 at 20iterations 4.7719222E-04 7.8117371E-02 at 30iterations 3.5033714E-05 5.0868988E-03 at 40iterations 2.6266850E-06 4.9209595E-04 at 50iterations finished qdiffx linear iterations at : 17:14:07 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.6266850E-06 4.9209595E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:14:07 3.429u 0.172s 0:03.92 91.5% 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 Mon Oct 10 2011 at 17:14:07 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2874 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.700610 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): -30.70800 32.09300 ymin,ymax (A): -24.96600 24.76500 zmin,zma (A): -8.972000 37.86600 x,y,z range (A): 62.80100 49.73100 46.83800 scale (grids/A): 1.700610 object centre (A): 0.6925011 -0.1005001 14.44700 number of atom coordinates read : 2874 total number of charged atoms : 2733 net assigned charge : -0.9859747 assigned positive charge : 436.3431 centred at (gu) : 92.12905 90.04767 88.86122 assigned negative charge : -437.3301 centred at (gu) : 91.98161 89.57581 88.47391 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26431 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20276 mr = 42637 m= 2325 mr = 13716 m= 65 mr = 1239 m= 0 mr = 10 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1273 time to turn everything in is 0.3300000 number of dielectric boundary points 29807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21071 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) : 0.5668699 object centre at (A) : 0.6925011 -0.1005001 14.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7515450E-03 6.8236203E-03 midg,1,midg; midg,igrid,midg -2.3426967E-02 9.6868761E-03 1,midg,midg; igrid,midg,midg -9.2397295E-03 2.2102384E-02 gauss-seidel spectral radius is 0.9983192 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 17:14:08 rms-change max change #iterations 3.610648 179.6224 at 10iterations 1.546552 56.91645 at 20iterations 0.6629421 25.43233 at 30iterations 0.2855178 10.89039 at 40iterations 0.1231425 4.183972 at 50iterations 5.2986920E-02 1.913376 at 60iterations 2.2828128E-02 0.9641671 at 70iterations 9.7801778E-03 0.4229927 at 80iterations 4.2209723E-03 0.1517181 at 90iterations 1.8213077E-03 6.8243504E-02 at 100iterations 7.8519288E-04 2.7721405E-02 at 110iterations 3.3886952E-04 1.1783600E-02 at 120iterations finished qdiffx linear iterations at : 17:14:15 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 3.3886952E-04 1.1783600E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 17:14:15 7.757u 0.199s 0:08.30 95.6% 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 17:14:15 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2874 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.550915 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): -30.70800 32.09300 ymin,ymax (A): -24.96600 24.76500 zmin,zma (A): -8.972000 37.86600 x,y,z range (A): 62.80100 49.73100 46.83800 scale (grids/A): 2.550915 object centre (A): 0.6925011 -0.1005001 14.44700 number of atom coordinates read : 2874 total number of charged atoms : 2733 net assigned charge : -0.9859747 assigned positive charge : 436.3431 centred at (gu) : 93.19331 90.07138 88.29166 assigned negative charge : -437.3301 centred at (gu) : 92.97232 89.36358 87.71072 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 150178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26431 grid for indexing accessible points = 1.400000 m= 68638 mr = 104340 m= 20598 mr = 53638 m= 3739 mr = 15337 m= 318 mr = 2528 m= 2 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4086 time to turn everything in is 0.8000000 number of dielectric boundary points 67463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21841 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) : 1.700610 object centre at (A) : 0.6925011 -0.1005001 14.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0181089E-02 6.8424799E-02 midg,1,midg; midg,igrid,midg -0.2898842 0.1595846 1,midg,midg; igrid,midg,midg 7.2434619E-02 0.4170840 gauss-seidel spectral radius is 0.9991798 estimated iterations to convergence 276 setup time was (sec) 1.040000 now iterating at: 17:14:17 rms-change max change #iterations 9.226775 379.5637 at 10iterations 5.250713 124.4797 at 20iterations 2.974086 74.29344 at 30iterations 1.679553 39.46746 at 40iterations 0.9461277 21.09490 at 50iterations 0.5303110 14.40511 at 60iterations 0.2974946 6.548527 at 70iterations 0.1666790 3.428512 at 80iterations 9.3236580E-02 1.952255 at 90iterations 5.2037317E-02 1.141997 at 100iterations 2.9098623E-02 0.6085081 at 110iterations 1.6250024E-02 0.3468335 at 120iterations 9.0732547E-03 0.1802912 at 130iterations 5.0565065E-03 0.1148052 at 140iterations 2.8103685E-03 5.7197571E-02 at 150iterations 1.5697833E-03 3.4869194E-02 at 160iterations 8.7669684E-04 1.7811775E-02 at 170iterations 4.8861443E-04 1.0335922E-02 at 180iterations finished qdiffx linear iterations at : 17:14:28 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 4.8861443E-04 1.0335922E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 17:14:28 12.326u 0.186s 0:12.93 96.6% 0+0k 0+0io 0pf+0w