Sat Oct 8 15:07:50 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 15:07:50 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3228 !!! WARNING: SEP 61 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-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 : 3079 net assigned charge : 3.025007 assigned positive charge : 482.1098 centred at (gu) : 91.78510 88.77258 89.99680 assigned negative charge : -479.0862 centred at (gu) : 91.84124 88.80255 89.99045 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 9603 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8038799E-10 1.5186616E-09 midg,1,midg; midg,igrid,midg 3.3314043E-09 -7.6014074E-12 1,midg,midg; igrid,midg,midg 2.4207316E-09 -1.7889434E-09 gauss-seidel spectral radius is 0.9855878 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 15:07:50 rms-change max change #iterations 0.1184524 20.51532 at 10iterations 1.0086998E-02 1.425312 at 20iterations 8.7664492E-04 0.1387453 at 30iterations 8.2838924E-05 1.1680603E-02 at 40iterations 1.0329466E-05 1.5088320E-03 at 50iterations finished qdiffx linear iterations at : 15:07:53 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0329466E-05 1.5088320E-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) 3.430000 DelPhi exited at 15:07:54 3.437u 0.227s 0:03.96 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 15:07:54 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3228 !!! WARNING: SEP 61 has a net charge of -0.4750 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: 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 : 3079 net assigned charge : 3.025007 assigned positive charge : 482.1098 centred at (gu) : 95.35472 86.31669 89.98968 assigned negative charge : -479.0862 centred at (gu) : 95.52357 86.40741 89.97115 start vw surface at 0.1800000 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 = 0.2500000 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 0.7100000 number of grid points assigned charge 24064 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 -3.1332627E-03 -2.1838088E-02 midg,1,midg; midg,igrid,midg 8.8763144E-03 6.2091784E-03 1,midg,midg; igrid,midg,midg 2.7941486E-02 1.5508479E-02 gauss-seidel spectral radius is 0.9985216 estimated iterations to convergence 206 setup time was (sec) 0.8800000 now iterating at: 15:07:55 rms-change max change #iterations 4.252605 191.1129 at 10iterations 1.926849 62.55713 at 20iterations 0.8716894 28.07989 at 30iterations 0.3982554 12.29550 at 40iterations 0.1808819 5.615284 at 50iterations 8.2278349E-02 2.469822 at 60iterations 3.7320700E-02 1.118787 at 70iterations 1.6965548E-02 0.4866552 at 80iterations 7.7277333E-03 0.2644081 at 90iterations 3.5235314E-03 0.1067209 at 100iterations 1.6025874E-03 5.0918579E-02 at 110iterations 7.3089672E-04 2.1320343E-02 at 120iterations finished qdiffx linear iterations at : 15:08:02 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 7.3089672E-04 2.1320343E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 15:08:02 7.863u 0.245s 0:08.46 95.7% 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 15:08:02 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3228 !!! WARNING: SEP 61 has a net charge of -0.4750 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: 2.692301 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 : 3079 net assigned charge : 3.025007 assigned positive charge : 482.1098 centred at (gu) : 98.03197 84.47475 89.98434 assigned negative charge : -479.0862 centred at (gu) : 98.28509 84.61101 89.95662 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 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 = 0.8000000 no. cavity mid-points inaccessible to solvent = 3668 time to turn everything in is 1.390000 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 1.530000 number of grid points assigned charge 24627 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 -4.0885672E-02 -0.3086584 midg,1,midg; midg,igrid,midg 3.6230821E-02 7.9300940E-02 1,midg,midg; igrid,midg,midg 0.3337046 0.3935694 gauss-seidel spectral radius is 0.9992380 estimated iterations to convergence 286 setup time was (sec) 1.710000 now iterating at: 15:08:04 rms-change max change #iterations 10.15865 353.9137 at 10iterations 5.885400 126.5591 at 20iterations 3.370981 72.09731 at 30iterations 1.937524 34.31638 at 40iterations 1.107739 20.65297 at 50iterations 0.6323850 11.76983 at 60iterations 0.3616111 6.305616 at 70iterations 0.2067075 3.639520 at 80iterations 0.1176676 2.079320 at 90iterations 6.7094676E-02 1.294901 at 100iterations 3.8319603E-02 0.6570177 at 110iterations 2.1830628E-02 0.3835602 at 120iterations 1.2433188E-02 0.2254744 at 130iterations 7.1143289E-03 0.1350346 at 140iterations 4.0698969E-03 7.5222015E-02 at 150iterations 2.3222601E-03 4.8202515E-02 at 160iterations 1.3312829E-03 2.4234772E-02 at 170iterations 7.6416606E-04 1.5604496E-02 at 180iterations finished qdiffx linear iterations at : 15:08:15 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 7.6416606E-04 1.5604496E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 15:08:16 12.976u 0.261s 0:13.59 97.3% 0+0k 0+0io 0pf+0w