Sat Oct 15 10:51:15 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 15 2011 at 10:51:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3240 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: 0.5946018 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): -27.21200 32.66000 ymin,ymax (A): 38.01600 90.90600 zmin,zma (A): 40.58700 88.29500 x,y,z range (A): 59.87200 52.89000 47.70800 scale (grids/A): 0.5946018 object centre (A): 2.724000 64.46100 64.44099 number of atom coordinates read : 3240 total number of charged atoms : 3091 net assigned charge : -10.99998 assigned positive charge : 477.3101 centred at (gu) : 90.63242 88.28109 88.96692 assigned negative charge : -488.3114 centred at (gu) : 90.60132 88.38778 89.02717 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7588 nv = 96 ne = 84 npr = 67468 no. pairs analyzed = 67468 no. exposed pairs = 3875 no. arc points = 26545 no. surface atoms = 1320 nbur = 1920 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= 349 mr = 4263 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3400000 number of dielectric boundary points 3645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2586 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1424096E-09 -5.0615330E-09 midg,1,midg; midg,igrid,midg 1.6364267E-10 -5.5756146E-09 1,midg,midg; igrid,midg,midg -4.5538946E-09 -3.2622547E-09 gauss-seidel spectral radius is 0.9854138 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 10:51:16 rms-change max change #iterations 0.1163783 14.86970 at 10iterations 1.0076217E-02 1.384743 at 20iterations 1.0645563E-03 0.1766729 at 30iterations 2.4554311E-04 3.3405304E-02 at 40iterations 8.8451910E-05 1.2660980E-02 at 50iterations finished qdiffx linear iterations at : 10:51:20 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 8.8451910E-05 1.2660980E-02 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 10:51:20 4.323u 0.276s 0:04.92 93.2% 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 15 2011 at 10:51:20 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 = 3240 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: 1.783805 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): -27.21200 32.66000 ymin,ymax (A): 38.01600 90.90600 zmin,zma (A): 40.58700 88.29500 x,y,z range (A): 59.87200 52.89000 47.70800 scale (grids/A): 1.783805 object centre (A): 2.724000 64.46100 64.44099 number of atom coordinates read : 3240 total number of charged atoms : 3091 net assigned charge : -10.99998 assigned positive charge : 477.3101 centred at (gu) : 91.89598 84.84219 86.89986 assigned negative charge : -488.3114 centred at (gu) : 91.80331 85.16277 87.08089 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26545 grid for indexing accessible points = 1.400000 m= 29094 mr = 59586 m= 4128 mr = 21260 m= 193 mr = 2444 m= 7 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2999 time to turn everything in is 0.6100000 number of dielectric boundary points 33691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 24101 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) : 0.5946018 object centre at (A) : 2.724000 64.46100 64.44099 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2636218E-03 -1.9771928E-02 midg,1,midg; midg,igrid,midg 1.1281265E-02 -2.9016480E-02 1,midg,midg; igrid,midg,midg -1.4211698E-02 -3.6249701E-03 gauss-seidel spectral radius is 0.9985055 estimated iterations to convergence 205 setup time was (sec) 0.9400000 now iterating at: 10:51:22 rms-change max change #iterations 4.254714 184.5101 at 10iterations 1.919137 64.10191 at 20iterations 0.8694602 26.57879 at 30iterations 0.3948344 12.84282 at 40iterations 0.1783406 5.499919 at 50iterations 8.1188664E-02 2.472988 at 60iterations 3.6765527E-02 1.128431 at 70iterations 1.6677018E-02 0.5031586 at 80iterations 7.5981021E-03 0.2546959 at 90iterations 3.4859974E-03 0.1028786 at 100iterations 1.6279443E-03 4.9509048E-02 at 110iterations 7.9149607E-04 2.9205322E-02 at 120iterations finished qdiffx linear iterations at : 10:51:30 total time elapsed so far: 9.820000 # loops : 120 mean,max change (kT/e) : 7.9149607E-04 2.9205322E-02 energy calculations done at 9.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.01000 DelPhi exited at 10:51:31 10.008u 0.302s 0:10.90 94.4% 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 10:51:31 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 = 3240 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: 2.675708 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): -27.21200 32.66000 ymin,ymax (A): 38.01600 90.90600 zmin,zma (A): 40.58700 88.29500 x,y,z range (A): 59.87200 52.89000 47.70800 scale (grids/A): 2.675708 object centre (A): 2.724000 64.46100 64.44099 number of atom coordinates read : 3240 total number of charged atoms : 3091 net assigned charge : -10.99998 assigned positive charge : 477.3101 centred at (gu) : 92.84373 82.26290 85.34937 assigned negative charge : -488.3114 centred at (gu) : 92.70466 82.74406 85.62104 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 193598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26545 grid for indexing accessible points = 1.400000 m= 96706 mr = 144431 m= 32510 mr = 79051 m= 7171 mr = 25590 m= 870 mr = 5351 m= 32 mr = 503 m= 0 mr = 7 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 9975 time to turn everything in is 1.570000 number of dielectric boundary points 75954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 24722 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) : 1.783805 object centre at (A) : 2.724000 64.46100 64.44099 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4928094E-02 -0.2346448 midg,1,midg; midg,igrid,midg 0.2200529 -0.3605372 1,midg,midg; igrid,midg,midg 3.4882624E-02 -0.1256536 gauss-seidel spectral radius is 0.9992284 estimated iterations to convergence 284 setup time was (sec) 1.930000 now iterating at: 10:51:34 rms-change max change #iterations 10.27050 320.5217 at 10iterations 5.960296 129.2981 at 20iterations 3.433233 74.44399 at 30iterations 1.967389 43.55377 at 40iterations 1.127311 23.12278 at 50iterations 0.6441563 10.81657 at 60iterations 0.3673754 7.959354 at 70iterations 0.2098760 4.289184 at 80iterations 0.1195531 2.111144 at 90iterations 6.8282925E-02 1.304523 at 100iterations 3.8878825E-02 0.7107131 at 110iterations 2.2132704E-02 0.4203501 at 120iterations 1.2622807E-02 0.2426491 at 130iterations 7.2141741E-03 0.1323853 at 140iterations 4.1495604E-03 7.3183060E-02 at 150iterations 2.4150740E-03 4.2062283E-02 at 160iterations 1.4354317E-03 2.7721405E-02 at 170iterations 8.8732463E-04 1.7283440E-02 at 180iterations finished qdiffx linear iterations at : 10:51:48 total time elapsed so far: 16.23000 # loops : 180 mean,max change (kT/e) : 8.8732463E-04 1.7283440E-02 energy calculations done at 16.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.40000 DelPhi exited at 10:51:48 16.404u 0.312s 0:17.02 98.1% 0+0k 0+0io 0pf+0w