Sat Oct 15 14:54:44 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 15 2011 at 14:54:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6309149 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): -31.03000 25.39600 ymin,ymax (A): 29.34200 83.04200 zmin,zma (A): 60.58900 108.5910 x,y,z range (A): 56.42600 53.70000 48.00200 scale (grids/A): 0.6309149 object centre (A): -2.816999 56.19200 84.59000 number of atom coordinates read : 2746 total number of charged atoms : 2605 net assigned charge : 4.000027 assigned positive charge : 411.6426 centred at (gu) : 88.38913 91.98705 90.13950 assigned negative charge : -407.6436 centred at (gu) : 88.50084 92.04398 90.18577 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7148 nv = 96 ne = 84 npr = 56627 no. pairs analyzed = 56627 no. exposed pairs = 3473 no. arc points = 24004 no. surface atoms = 1172 nbur = 1574 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3818 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2385 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8768 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4795975E-09 -2.7042856E-11 midg,1,midg; midg,igrid,midg 6.3751902E-09 -1.7869124E-09 1,midg,midg; igrid,midg,midg 2.1115655E-08 -4.3821990E-09 gauss-seidel spectral radius is 0.9869980 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 14:54:45 rms-change max change #iterations 0.1395305 26.25749 at 10iterations 1.3381944E-02 1.824581 at 20iterations 1.2905304E-03 0.1765823 at 30iterations 1.3147380E-04 2.0095825E-02 at 40iterations 1.6322108E-05 2.4757385E-03 at 50iterations finished qdiffx linear iterations at : 14:54:48 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 1.6322108E-05 2.4757385E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:54:49 3.624u 0.199s 0:04.26 89.4% 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 15 2011 at 14:54:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.892745 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): -31.03000 25.39600 ymin,ymax (A): 29.34200 83.04200 zmin,zma (A): 60.58900 108.5910 x,y,z range (A): 56.42600 53.70000 48.00200 scale (grids/A): 1.892745 object centre (A): -2.816999 56.19200 84.59000 number of atom coordinates read : 2746 total number of charged atoms : 2605 net assigned charge : 4.000027 assigned positive charge : 411.6426 centred at (gu) : 85.16663 95.96075 90.41814 assigned negative charge : -407.6436 centred at (gu) : 85.50227 96.13204 90.55717 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24004 grid for indexing accessible points = 1.400000 m= 27210 mr = 53124 m= 4321 mr = 19335 m= 237 mr = 2414 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 0.3800000 number of dielectric boundary points 34307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20475 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) : 0.6309149 object centre at (A) : -2.816999 56.19200 84.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1180134E-02 5.1831375E-03 midg,1,midg; midg,igrid,midg 1.4416822E-02 -7.8465510E-03 1,midg,midg; igrid,midg,midg 4.0939301E-02 9.2961490E-03 gauss-seidel spectral radius is 0.9986297 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 14:54:50 rms-change max change #iterations 4.331040 182.5853 at 10iterations 2.018245 64.07010 at 20iterations 0.9431455 37.53445 at 30iterations 0.4431078 15.14875 at 40iterations 0.2071171 7.121964 at 50iterations 9.7068593E-02 3.111467 at 60iterations 4.5236163E-02 1.474799 at 70iterations 2.1192444E-02 0.7013545 at 80iterations 9.9130766E-03 0.3272953 at 90iterations 4.6476922E-03 0.1419716 at 100iterations 2.1763411E-03 7.2472200E-02 at 110iterations 1.0192849E-03 3.1658173E-02 at 120iterations finished qdiffx linear iterations at : 14:55:04 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 1.0192849E-03 3.1658173E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 14:55:05 8.214u 0.229s 0:16.32 51.6% 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 15 2011 at 14:55:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 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: 2.839117 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): -31.03000 25.39600 ymin,ymax (A): 29.34200 83.04200 zmin,zma (A): 60.58900 108.5910 x,y,z range (A): 56.42600 53.70000 48.00200 scale (grids/A): 2.839117 object centre (A): -2.816999 56.19200 84.59000 number of atom coordinates read : 2746 total number of charged atoms : 2605 net assigned charge : 4.000027 assigned positive charge : 411.6426 centred at (gu) : 82.74993 98.94107 90.62695 assigned negative charge : -407.6436 centred at (gu) : 83.25345 99.19793 90.83563 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24004 grid for indexing accessible points = 1.400000 m= 88119 mr = 129829 m= 32079 mr = 70399 m= 7749 mr = 24880 m= 995 mr = 5454 m= 73 mr = 532 m= 0 mr = 40 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 895 time to turn everything in is 1.000000 number of dielectric boundary points 77293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 20823 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) : 1.892745 object centre at (A) : -2.816999 56.19200 84.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5984856E-02 4.5160707E-02 midg,1,midg; midg,igrid,midg 0.2214895 -0.1465250 1,midg,midg; igrid,midg,midg 0.5045286 8.8744082E-02 gauss-seidel spectral radius is 0.9992635 estimated iterations to convergence 291 setup time was (sec) 1.260000 now iterating at: 14:55:07 rms-change max change #iterations 10.26412 318.6536 at 10iterations 6.035655 162.2694 at 20iterations 3.522473 98.85219 at 30iterations 2.051507 40.10312 at 40iterations 1.192364 21.27110 at 50iterations 0.6923997 17.25230 at 60iterations 0.4004134 8.728466 at 70iterations 0.2312449 4.038273 at 80iterations 0.1336350 2.344124 at 90iterations 7.7101037E-02 1.585709 at 100iterations 4.4414748E-02 0.7410355 at 110iterations 2.5602397E-02 0.4427981 at 120iterations 1.4759559E-02 0.2624874 at 130iterations 8.4992498E-03 0.1542315 at 140iterations 4.8972587E-03 8.9653015E-02 at 150iterations 2.8131781E-03 5.0591469E-02 at 160iterations 1.6189583E-03 3.0151367E-02 at 170iterations 9.3228108E-04 1.5911102E-02 at 180iterations finished qdiffx linear iterations at : 14:55:31 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 9.3228108E-04 1.5911102E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 14:55:32 13.335u 0.236s 0:26.37 51.4% 0+0k 0+0io 0pf+0w