Sat Oct 8 15:07:23 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 Sat Oct 8 2011 at 15:07:23 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3228 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: 0.5982892 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): -82.91800 -23.41500 ymin,ymax (A): -23.53700 27.18800 zmin,zma (A): 34.03900 89.08000 x,y,z range (A): 59.50300 50.72500 55.04100 scale (grids/A): 0.5982892 object centre (A): -53.16650 1.825500 61.55950 number of atom coordinates read : 3228 total number of charged atoms : 3081 net assigned charge : 3.500007 assigned positive charge : 481.7898 centred at (gu) : 91.78800 88.76987 89.99945 assigned negative charge : -478.2912 centred at (gu) : 91.84627 88.79770 89.99400 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7581 nv = 96 ne = 84 npr = 66676 no. pairs analyzed = 66676 no. exposed pairs = 3681 no. arc points = 25782 no. surface atoms = 1254 nbur = 1974 mkacc time = 0.1400000 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= 308 mr = 4287 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2658 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9605 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2129852E-09 1.6754336E-09 midg,1,midg; midg,igrid,midg 3.4657441E-09 2.1164286E-10 1,midg,midg; igrid,midg,midg 2.6071207E-09 -1.6331894E-09 gauss-seidel spectral radius is 0.9855878 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 15:07:24 rms-change max change #iterations 0.1182557 20.70168 at 10iterations 1.0089088E-02 1.396364 at 20iterations 8.9274877E-04 0.1436005 at 30iterations 8.9596120E-05 1.2705982E-02 at 40iterations 1.2471740E-05 1.9451231E-03 at 50iterations finished qdiffx linear iterations at : 15:07:27 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.2471740E-05 1.9451231E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 15:07:27 3.443u 0.220s 0:03.97 92.1% 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 15:07:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3228 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.794868 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): -82.91800 -23.41500 ymin,ymax (A): -23.53700 27.18800 zmin,zma (A): 34.03900 89.08000 x,y,z range (A): 59.50300 50.72500 55.04100 scale (grids/A): 1.794868 object centre (A): -53.16650 1.825500 61.55950 number of atom coordinates read : 3228 total number of charged atoms : 3081 net assigned charge : 3.500007 assigned positive charge : 481.7898 centred at (gu) : 95.36345 86.30854 89.99759 assigned negative charge : -478.2912 centred at (gu) : 95.53870 86.39284 89.98181 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83318 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25782 grid for indexing accessible points = 1.400000 m= 27696 mr = 59441 m= 3339 mr = 20189 m= 126 mr = 1864 m= 0 mr = 20 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 0.5800000 number of dielectric boundary points 32965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 24078 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) : 0.5982892 object centre at (A) : -53.16650 1.825500 61.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3129198E-03 -2.1374751E-02 midg,1,midg; midg,igrid,midg 9.3474165E-03 6.8918560E-03 1,midg,midg; igrid,midg,midg 2.8656825E-02 1.6156141E-02 gauss-seidel spectral radius is 0.9985216 estimated iterations to convergence 206 setup time was (sec) 0.8700000 now iterating at: 15:07:28 rms-change max change #iterations 4.243760 191.1129 at 10iterations 1.922229 62.55724 at 20iterations 0.8696378 28.07975 at 30iterations 0.3973449 12.13817 at 40iterations 0.1805167 5.569000 at 50iterations 8.2076631E-02 2.480034 at 60iterations 3.7236180E-02 1.118603 at 70iterations 1.6929345E-02 0.4876696 at 80iterations 7.7141318E-03 0.2634373 at 90iterations 3.5170927E-03 0.1068478 at 100iterations 1.5996634E-03 5.1162720E-02 at 110iterations 7.3006900E-04 2.1150589E-02 at 120iterations finished qdiffx linear iterations at : 15:07:35 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 7.3006900E-04 2.1150589E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 15:07:36 7.956u 0.270s 0:08.54 96.2% 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 15:07:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3228 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.692301 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): -82.91800 -23.41500 ymin,ymax (A): -23.53700 27.18800 zmin,zma (A): 34.03900 89.08000 x,y,z range (A): 59.50300 50.72500 55.04100 scale (grids/A): 2.692301 object centre (A): -53.16650 1.825500 61.55950 number of atom coordinates read : 3228 total number of charged atoms : 3081 net assigned charge : 3.500007 assigned positive charge : 481.7898 centred at (gu) : 98.04505 84.46252 89.99619 assigned negative charge : -478.2912 centred at (gu) : 98.30780 84.58915 89.97261 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 193303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25782 grid for indexing accessible points = 1.400000 m= 94404 mr = 144285 m= 29743 mr = 77399 m= 5551 mr = 23426 m= 507 mr = 3923 m= 17 mr = 228 m= 0 mr = 4 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 3668 time to turn everything in is 1.420000 number of dielectric boundary points 74260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 24643 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) : 1.794868 object centre at (A) : -53.16650 1.825500 61.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0849133E-02 -0.3036016 midg,1,midg; midg,igrid,midg 4.1965071E-02 8.7301500E-02 1,midg,midg; igrid,midg,midg 0.3424944 0.4017151 gauss-seidel spectral radius is 0.9992380 estimated iterations to convergence 286 setup time was (sec) 1.730000 now iterating at: 15:07:38 rms-change max change #iterations 10.13853 353.9138 at 10iterations 5.874247 126.5591 at 20iterations 3.364538 71.88878 at 30iterations 1.933859 34.32225 at 40iterations 1.105675 20.56725 at 50iterations 0.6311702 11.89578 at 60iterations 0.3609541 6.241127 at 70iterations 0.2063611 3.632314 at 80iterations 0.1174737 2.053070 at 90iterations 6.6987947E-02 1.312619 at 100iterations 3.8259640E-02 0.6647635 at 110iterations 2.1803409E-02 0.3852463 at 120iterations 1.2422233E-02 0.2241154 at 130iterations 7.1117929E-03 0.1366024 at 140iterations 4.0721335E-03 7.4272156E-02 at 150iterations 2.3260855E-03 4.8950195E-02 at 160iterations 1.3360983E-03 2.3517609E-02 at 170iterations 7.6949270E-04 1.6087055E-02 at 180iterations finished qdiffx linear iterations at : 15:07:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 7.6949270E-04 1.6087055E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 15:07:50 12.971u 0.252s 0:13.57 97.4% 0+0k 0+0io 0pf+0w