Mon Oct 10 00:14:04 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 Mon Oct 10 2011 at 00:14:04 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3792 !!! WARNING: HIR 134 has a net charge of 0.5140 !!! WARNING: HIR 135 has a net charge of 0.5140 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: GLM 254 has a net charge of -0.0940 !!! WARNING: ZN1 1098 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5716671 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): 32.64100 94.91500 ymin,ymax (A): -2.142000 56.44400 zmin,zma (A): -32.67400 27.36800 x,y,z range (A): 62.27400 58.58600 60.04200 scale (grids/A): 0.5716671 object centre (A): 63.77800 27.15100 -2.653000 number of atom coordinates read : 3792 total number of charged atoms : 3665 net assigned charge : 6.534051 assigned positive charge : 583.0640 centred at (gu) : 88.20449 89.62988 90.42013 assigned negative charge : -576.5322 centred at (gu) : 88.30371 89.69159 90.45448 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7900 nv = 96 ne = 84 npr = 77300 no. pairs analyzed = 77300 no. exposed pairs = 4383 no. arc points = 30379 no. surface atoms = 1481 nbur = 2311 mkacc time = 0.1800000 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 = 1.512000 m= 314 mr = 4471 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3117 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10349 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5881296E-09 2.9818173E-10 midg,1,midg; midg,igrid,midg 2.5471176E-09 -2.8884928E-10 1,midg,midg; igrid,midg,midg 4.8091211E-09 -7.2937761E-10 gauss-seidel spectral radius is 0.9842636 estimated iterations to convergence 66 setup time was (sec) 0.6600000 now iterating at: 00:14:05 rms-change max change #iterations 0.1060621 13.38950 at 10iterations 8.4781107E-03 1.191117 at 20iterations 7.8331592E-04 0.1322060 at 30iterations 1.3534258E-04 2.2220612E-02 at 40iterations 3.2982822E-05 6.0214996E-03 at 50iterations finished qdiffx linear iterations at : 00:14:08 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.2982822E-05 6.0214996E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 00:14:08 3.490u 0.149s 0:03.91 92.8% 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 Mon Oct 10 2011 at 00:14:08 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3792 !!! WARNING: HIR 134 has a net charge of 0.5140 !!! WARNING: HIR 135 has a net charge of 0.5140 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: GLM 254 has a net charge of -0.0940 !!! WARNING: ZN1 1098 has a net charge of 1.4000 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: 1.715001 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): 32.64100 94.91500 ymin,ymax (A): -2.142000 56.44400 zmin,zma (A): -32.67400 27.36800 x,y,z range (A): 62.27400 58.58600 60.04200 scale (grids/A): 1.715001 object centre (A): 63.77800 27.15100 -2.653000 number of atom coordinates read : 3792 total number of charged atoms : 3665 net assigned charge : 6.534051 assigned positive charge : 583.0640 centred at (gu) : 84.61202 88.88870 91.25902 assigned negative charge : -576.5322 centred at (gu) : 84.91060 89.07409 91.36282 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 87965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30379 grid for indexing accessible points = 1.400000 m= 27856 mr = 62743 m= 3061 mr = 20227 m= 84 mr = 1677 m= 0 mr = 16 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1124 time to turn everything in is 0.6200000 number of dielectric boundary points 34303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 28382 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) : 0.5716671 object centre at (A) : 63.77800 27.15100 -2.653000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7746575E-02 -1.1720269E-02 midg,1,midg; midg,igrid,midg 2.1339122E-02 9.1559449E-03 1,midg,midg; igrid,midg,midg 2.7203823E-02 -6.8369592E-03 gauss-seidel spectral radius is 0.9984226 estimated iterations to convergence 200 setup time was (sec) 0.9100000 now iterating at: 00:14:09 rms-change max change #iterations 4.318615 167.5659 at 10iterations 1.908373 68.37457 at 20iterations 0.8446909 25.88567 at 30iterations 0.3756315 12.42101 at 40iterations 0.1655950 5.241626 at 50iterations 7.3543839E-02 2.289525 at 60iterations 3.2562032E-02 0.9766502 at 70iterations 1.4477896E-02 0.4618988 at 80iterations 6.4386749E-03 0.1947937 at 90iterations 2.8722843E-03 9.2765808E-02 at 100iterations 1.2824947E-03 4.2016029E-02 at 110iterations 5.7981774E-04 1.7456055E-02 at 120iterations finished qdiffx linear iterations at : 00:14:16 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 5.7981774E-04 1.7456055E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 00:14:16 7.698u 0.195s 0:08.38 94.0% 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 Mon Oct 10 2011 at 00:14:16 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3792 !!! WARNING: HIR 134 has a net charge of 0.5140 !!! WARNING: HIR 135 has a net charge of 0.5140 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: GLM 254 has a net charge of -0.0940 !!! WARNING: ZN1 1098 has a net charge of 1.4000 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: 2.572502 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): 32.64100 94.91500 ymin,ymax (A): -2.142000 56.44400 zmin,zma (A): -32.67400 27.36800 x,y,z range (A): 62.27400 58.58600 60.04200 scale (grids/A): 2.572502 object centre (A): 63.77800 27.15100 -2.653000 number of atom coordinates read : 3792 total number of charged atoms : 3665 net assigned charge : 6.534051 assigned positive charge : 583.0640 centred at (gu) : 81.91782 88.33276 91.88826 assigned negative charge : -576.5322 centred at (gu) : 82.36566 88.61097 92.04401 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 204962 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30379 grid for indexing accessible points = 1.400000 m= 96754 mr = 152915 m= 28220 mr = 79082 m= 5099 mr = 22211 m= 455 mr = 3640 m= 9 mr = 246 m= 0 mr = 2 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 3807 time to turn everything in is 1.540000 number of dielectric boundary points 77403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 29305 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) : 1.715001 object centre at (A) : 63.77800 27.15100 -2.653000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8195643 -0.2727847 midg,1,midg; midg,igrid,midg 0.3296612 0.1349904 1,midg,midg; igrid,midg,midg 3.7206315E-02 -9.8358892E-02 gauss-seidel spectral radius is 0.9992133 estimated iterations to convergence 281 setup time was (sec) 1.870000 now iterating at: 00:14:19 rms-change max change #iterations 10.54848 331.0944 at 10iterations 6.030100 136.8521 at 20iterations 3.442371 65.36732 at 30iterations 1.955624 40.56445 at 40iterations 1.110784 23.44279 at 50iterations 0.6292317 12.60930 at 60iterations 0.3568115 6.077564 at 70iterations 0.2014447 3.577872 at 80iterations 0.1141796 2.236610 at 90iterations 6.4513765E-02 1.237736 at 100iterations 3.6514372E-02 0.6514931 at 110iterations 2.0592585E-02 0.3915482 at 120iterations 1.1662742E-02 0.2144215 at 130iterations 6.6121570E-03 0.1281080 at 140iterations 3.7378774E-03 6.7184180E-02 at 150iterations 2.1244606E-03 3.6072731E-02 at 160iterations 1.2120459E-03 2.2760391E-02 at 170iterations 6.9377746E-04 1.2088776E-02 at 180iterations finished qdiffx linear iterations at : 00:14:30 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 6.9377746E-04 1.2088776E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 00:14:30 13.082u 0.192s 0:13.58 97.7% 0+0k 0+0io 0pf+0w