Sat Oct 8 17:27:18 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 Sat Oct 8 2011 at 17:27:19 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3753 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5530269 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): -1.932000 60.53100 ymin,ymax (A): -18.47100 44.41600 zmin,zma (A): -5.423000 58.95000 x,y,z range (A): 62.46300 62.88700 64.37300 scale (grids/A): 0.5530269 object centre (A): 29.29950 12.97250 26.76350 number of atom coordinates read : 3753 total number of charged atoms : 3603 net assigned charge : -7.999968 assigned positive charge : 571.3493 centred at (gu) : 88.84684 86.67959 90.46197 assigned negative charge : -579.3519 centred at (gu) : 88.90271 86.67167 90.46053 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7549 nv = 96 ne = 84 npr = 75719 no. pairs analyzed = 75719 no. exposed pairs = 4861 no. arc points = 34390 no. surface atoms = 1612 nbur = 2141 mkacc time = 0.2600000 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 = 1.568000 m= 331 mr = 3909 m= 0 mr = 15 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 3956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3474 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 9856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9571420E-10 -7.0601902E-10 midg,1,midg; midg,igrid,midg -1.6518509E-09 -2.6067837E-10 1,midg,midg; igrid,midg,midg -3.5690149E-11 -9.6192709E-10 gauss-seidel spectral radius is 0.9832001 estimated iterations to convergence 63 setup time was (sec) 0.8600000 now iterating at: 17:27:20 rms-change max change #iterations 9.0240039E-02 15.80391 at 10iterations 6.3354769E-03 0.9597988 at 20iterations 5.1182846E-04 7.7758789E-02 at 30iterations 7.5378361E-05 1.4533043E-02 at 40iterations 1.8264500E-05 3.5595894E-03 at 50iterations finished qdiffx linear iterations at : 17:27:23 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 1.8264500E-05 3.5595894E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 17:27:24 4.704u 0.444s 0:05.46 94.1% 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 17:27:24 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3753 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.659081 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): -1.932000 60.53100 ymin,ymax (A): -18.47100 44.41600 zmin,zma (A): -5.423000 58.95000 x,y,z range (A): 62.46300 62.88700 64.37300 scale (grids/A): 1.659081 object centre (A): 29.29950 12.97250 26.76350 number of atom coordinates read : 3753 total number of charged atoms : 3603 net assigned charge : -7.999968 assigned positive charge : 571.3493 centred at (gu) : 86.53948 80.03742 91.38449 assigned negative charge : -579.3519 centred at (gu) : 86.70773 80.01447 91.38113 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 83265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26479 mr = 56616 m= 2884 mr = 18110 m= 87 mr = 1317 m= 0 mr = 7 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.8600000 number of dielectric boundary points 36665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 27697 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) : 0.5530269 object centre at (A) : 29.29950 12.97250 26.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2775697E-03 -4.0214290E-03 midg,1,midg; midg,igrid,midg -2.6068004E-02 -7.8739300E-03 1,midg,midg; igrid,midg,midg -1.2156799E-02 -3.0090287E-02 gauss-seidel spectral radius is 0.9983170 estimated iterations to convergence 194 setup time was (sec) 1.220000 now iterating at: 17:27:26 rms-change max change #iterations 3.999155 180.0078 at 10iterations 1.721331 62.40504 at 20iterations 0.7405735 23.97979 at 30iterations 0.3192810 10.07460 at 40iterations 0.1376035 4.559990 at 50iterations 5.9167430E-02 1.967941 at 60iterations 2.5545880E-02 0.8076227 at 70iterations 1.1014356E-02 0.4111938 at 80iterations 4.7692303E-03 0.1664177 at 90iterations 2.0564701E-03 6.6894531E-02 at 100iterations 8.9582236E-04 3.1555176E-02 at 110iterations 3.9299371E-04 1.1998177E-02 at 120iterations finished qdiffx linear iterations at : 17:27:36 total time elapsed so far: 11.24000 # loops : 120 mean,max change (kT/e) : 3.9299371E-04 1.1998177E-02 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 17:27:36 11.459u 0.476s 0:12.21 97.6% 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 Sat Oct 8 2011 at 17:27:36 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3753 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.488621 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): -1.932000 60.53100 ymin,ymax (A): -18.47100 44.41600 zmin,zma (A): -5.423000 58.95000 x,y,z range (A): 62.46300 62.88700 64.37300 scale (grids/A): 2.488621 object centre (A): 29.29950 12.97250 26.76350 number of atom coordinates read : 3753 total number of charged atoms : 3603 net assigned charge : -7.999968 assigned positive charge : 571.3493 centred at (gu) : 84.80901 75.05587 92.07664 assigned negative charge : -579.3519 centred at (gu) : 85.06164 75.02160 92.07169 start vw surface at 0.1900000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 193400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 90873 mr = 138698 m= 26288 mr = 71427 m= 4380 mr = 19504 m= 321 mr = 2706 m= 7 mr = 116 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 846 time to turn everything in is 2.150000 number of dielectric boundary points 82819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 28788 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) : 1.659081 object centre at (A) : 29.29950 12.97250 26.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2555744E-02 0.1480127 midg,1,midg; midg,igrid,midg -0.4129983 -0.1013003 1,midg,midg; igrid,midg,midg -0.1867874 -0.5678975 gauss-seidel spectral radius is 0.9991950 estimated iterations to convergence 278 setup time was (sec) 2.540000 now iterating at: 17:27:39 rms-change max change #iterations 10.24441 291.6641 at 10iterations 5.880609 158.6630 at 20iterations 3.362391 74.50465 at 30iterations 1.910166 38.18954 at 40iterations 1.083454 20.46510 at 50iterations 0.6110213 12.71922 at 60iterations 0.3456756 7.851719 at 70iterations 0.1949679 3.795306 at 80iterations 0.1096854 2.082642 at 90iterations 6.1546978E-02 1.254256 at 100iterations 3.4650188E-02 0.6244717 at 110iterations 1.9483916E-02 0.4082026 at 120iterations 1.0948907E-02 0.1951466 at 130iterations 6.1527425E-03 0.1195936 at 140iterations 3.4530954E-03 7.3811054E-02 at 150iterations 1.9441196E-03 3.8371086E-02 at 160iterations 1.0952577E-03 1.9033432E-02 at 170iterations 6.1744772E-04 1.2282848E-02 at 180iterations finished qdiffx linear iterations at : 17:27:59 total time elapsed so far: 22.06000 # loops : 180 mean,max change (kT/e) : 6.1744772E-04 1.2282848E-02 energy calculations done at 22.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.28000 DelPhi exited at 17:27:59 22.285u 0.478s 0:23.04 98.7% 0+0k 0+0io 0pf+0w