Sat Oct 8 13:17:13 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 13:17:13 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5838267 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): 12.27100 64.43600 ymin,ymax (A): 1.851000 55.99700 zmin,zma (A): 85.05800 146.0350 x,y,z range (A): 52.16500 54.14600 60.97701 scale (grids/A): 0.5838267 object centre (A): 38.35350 28.92400 115.5465 number of atom coordinates read : 3056 total number of charged atoms : 2908 net assigned charge : -3.773964 assigned positive charge : 454.6667 centred at (gu) : 90.31914 92.13244 90.54275 assigned negative charge : -458.4419 centred at (gu) : 90.16788 92.07468 90.50806 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6851 nv = 96 ne = 84 npr = 62154 no. pairs analyzed = 62154 no. exposed pairs = 3835 no. arc points = 26757 no. surface atoms = 1276 nbur = 1780 mkacc time = 0.1600000 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 = 1.456000 m= 283 mr = 3719 m= 0 mr = 18 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2762 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8854 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6586826E-09 -1.0947038E-10 midg,1,midg; midg,igrid,midg -1.5182011E-09 8.4493734E-10 1,midg,midg; igrid,midg,midg -4.5773523E-09 3.0451546E-09 gauss-seidel spectral radius is 0.9848614 estimated iterations to convergence 67 setup time was (sec) 0.6900000 now iterating at: 13:17:14 rms-change max change #iterations 0.1032226 17.15339 at 10iterations 8.9758905E-03 1.218430 at 20iterations 1.4288620E-03 0.3117294 at 30iterations 5.7045172E-04 0.1218891 at 40iterations 2.5691537E-04 5.5540085E-02 at 50iterations finished qdiffx linear iterations at : 13:17:18 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 2.5691537E-04 5.5540085E-02 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 13:17:19 4.580u 0.411s 0:05.26 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 13:17:19 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.751480 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): 12.27100 64.43600 ymin,ymax (A): 1.851000 55.99700 zmin,zma (A): 85.05800 146.0350 x,y,z range (A): 52.16500 54.14600 60.97701 scale (grids/A): 1.751480 object centre (A): 38.35350 28.92400 115.5465 number of atom coordinates read : 3056 total number of charged atoms : 2908 net assigned charge : -3.773964 assigned positive charge : 454.6667 centred at (gu) : 90.95657 96.39629 91.62715 assigned negative charge : -458.4419 centred at (gu) : 90.50312 96.22350 91.52403 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26757 grid for indexing accessible points = 1.400000 m= 25043 mr = 52341 m= 3006 mr = 17994 m= 116 mr = 1674 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 776 time to turn everything in is 0.6100000 number of dielectric boundary points 31683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22618 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) : 0.5838267 object centre at (A) : 38.35350 28.92400 115.5465 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2186518E-02 4.8582517E-03 midg,1,midg; midg,igrid,midg -1.9959942E-02 -4.4962843E-03 1,midg,midg; igrid,midg,midg -7.4840412E-03 3.7512579E-03 gauss-seidel spectral radius is 0.9984370 estimated iterations to convergence 201 setup time was (sec) 0.9500000 now iterating at: 13:17:20 rms-change max change #iterations 3.933442 168.6450 at 10iterations 1.737260 67.93095 at 20iterations 0.7770664 27.39294 at 30iterations 0.3440303 11.88136 at 40iterations 0.1535006 5.047331 at 50iterations 6.8435788E-02 2.212376 at 60iterations 3.0571679E-02 1.107857 at 70iterations 1.3767375E-02 0.4211788 at 80iterations 6.3643567E-03 0.2040405 at 90iterations 3.1668341E-03 0.1166039 at 100iterations 1.7488176E-03 7.1868896E-02 at 110iterations 1.1102116E-03 4.6024323E-02 at 120iterations finished qdiffx linear iterations at : 13:17:30 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 1.1102116E-03 4.6024323E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 13:17:30 10.701u 0.455s 0:11.52 96.7% 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 13:17:30 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3056 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.627220 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): 12.27100 64.43600 ymin,ymax (A): 1.851000 55.99700 zmin,zma (A): 85.05800 146.0350 x,y,z range (A): 52.16500 54.14600 60.97701 scale (grids/A): 2.627220 object centre (A): 38.35350 28.92400 115.5465 number of atom coordinates read : 3056 total number of charged atoms : 2908 net assigned charge : -3.773964 assigned positive charge : 454.6667 centred at (gu) : 91.43465 99.59430 92.44041 assigned negative charge : -458.4419 centred at (gu) : 90.75461 99.33521 92.28599 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 174957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26757 grid for indexing accessible points = 1.400000 m= 84649 mr = 127246 m= 26971 mr = 68406 m= 5030 mr = 21252 m= 475 mr = 3454 m= 9 mr = 250 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2746 time to turn everything in is 1.640000 number of dielectric boundary points 71483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 23245 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) : 1.751480 object centre at (A) : 38.35350 28.92400 115.5465 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2930724 3.0052331E-03 midg,1,midg; midg,igrid,midg -0.3162124 -4.8456751E-02 1,midg,midg; igrid,midg,midg -1.8538788E-02 -4.4993903E-02 gauss-seidel spectral radius is 0.9992130 estimated iterations to convergence 281 setup time was (sec) 1.980000 now iterating at: 13:17:33 rms-change max change #iterations 9.673708 286.7137 at 10iterations 5.579823 129.6065 at 20iterations 3.200154 74.54903 at 30iterations 1.831373 51.01392 at 40iterations 1.046577 20.71214 at 50iterations 0.5952326 12.38729 at 60iterations 0.3390680 7.052261 at 70iterations 0.1928101 3.637558 at 80iterations 0.1091589 2.578499 at 90iterations 6.2011685E-02 1.159256 at 100iterations 3.5129528E-02 0.6747456 at 110iterations 1.9992016E-02 0.3781433 at 120iterations 1.1422890E-02 0.2425022 at 130iterations 6.5762657E-03 0.1376190 at 140iterations 3.8638695E-03 9.3521118E-02 at 150iterations 2.3685950E-03 5.3497314E-02 at 160iterations 1.5413089E-03 3.8558960E-02 at 170iterations 1.0871101E-03 2.8991699E-02 at 180iterations finished qdiffx linear iterations at : 13:17:48 total time elapsed so far: 17.74000 # loops : 180 mean,max change (kT/e) : 1.0871101E-03 2.8991699E-02 energy calculations done at 17.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.91000 DelPhi exited at 13:17:49 17.910u 0.469s 0:18.65 98.4% 0+0k 0+0io 0pf+0w