Mon Oct 10 14:01:12 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 Mon Oct 10 2011 at 14:01:12 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 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: 0.5883033 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): -16.45200 34.17500 ymin,ymax (A): -1.758000 46.55000 zmin,zma (A): -6.288000 54.22500 x,y,z range (A): 50.62700 48.30800 60.51300 scale (grids/A): 0.5883033 object centre (A): 8.861502 22.39600 23.96850 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 1.500008 assigned positive charge : 476.2468 centred at (gu) : 90.47689 89.47734 91.35226 assigned negative charge : -474.7480 centred at (gu) : 90.39434 89.52992 91.38741 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7267 nv = 96 ne = 84 npr = 66073 no. pairs analyzed = 66073 no. exposed pairs = 3723 no. arc points = 25489 no. surface atoms = 1270 nbur = 1933 mkacc time = 0.1700000 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 = 1.484000 m= 343 mr = 4128 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3600000 number of dielectric boundary points 3461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2573 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9241 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1040601E-09 -9.1500824E-10 midg,1,midg; midg,igrid,midg 2.3028481E-09 -1.0580725E-09 1,midg,midg; igrid,midg,midg -1.9074566E-09 3.2941971E-09 gauss-seidel spectral radius is 0.9850969 estimated iterations to convergence 67 setup time was (sec) 0.6100000 now iterating at: 14:01:13 rms-change max change #iterations 0.1097068 16.06145 at 10iterations 9.2987148E-03 1.281460 at 20iterations 9.2415570E-04 0.1268864 at 30iterations 1.4336369E-04 2.4219513E-02 at 40iterations 3.3139469E-05 6.0119629E-03 at 50iterations finished qdiffx linear iterations at : 14:01:16 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 3.3139469E-05 6.0119629E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 14:01:17 4.497u 0.400s 0:05.37 91.0% 0+0k 0+0io 6pf+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 14:01:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 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: 1.764910 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): -16.45200 34.17500 ymin,ymax (A): -1.758000 46.55000 zmin,zma (A): -6.288000 54.22500 x,y,z range (A): 50.62700 48.30800 60.51300 scale (grids/A): 1.764910 object centre (A): 8.861502 22.39600 23.96850 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 1.500008 assigned positive charge : 476.2468 centred at (gu) : 91.42968 88.43105 94.05582 assigned negative charge : -474.7480 centred at (gu) : 91.18269 88.58948 94.16198 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25489 grid for indexing accessible points = 1.400000 m= 28134 mr = 56251 m= 3839 mr = 20626 m= 122 mr = 2240 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 0.6300000 number of dielectric boundary points 32179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 23816 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) : 0.5883033 object centre at (A) : 8.861502 22.39600 23.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2210123E-02 -3.3759892E-02 midg,1,midg; midg,igrid,midg 8.1100110E-03 4.4007734E-03 1,midg,midg; igrid,midg,midg -9.7924741E-03 -1.2982487E-03 gauss-seidel spectral radius is 0.9984714 estimated iterations to convergence 203 setup time was (sec) 0.9500000 now iterating at: 14:01:18 rms-change max change #iterations 4.027435 160.9989 at 10iterations 1.796403 65.54185 at 20iterations 0.8049444 26.12030 at 30iterations 0.3619299 11.82422 at 40iterations 0.1618799 5.439009 at 50iterations 7.2829895E-02 2.655565 at 60iterations 3.2659646E-02 1.119079 at 70iterations 1.4716574E-02 0.4675598 at 80iterations 6.6242912E-03 0.2032280 at 90iterations 3.0014669E-03 9.6128464E-02 at 100iterations 1.3667304E-03 4.3123245E-02 at 110iterations 6.2915013E-04 2.2640705E-02 at 120iterations finished qdiffx linear iterations at : 14:01:28 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 6.2915013E-04 2.2640705E-02 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 14:01:29 10.679u 0.454s 0:11.88 93.6% 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 Mon Oct 10 2011 at 14:01:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 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: 2.647365 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): -16.45200 34.17500 ymin,ymax (A): -1.758000 46.55000 zmin,zma (A): -6.288000 54.22500 x,y,z range (A): 50.62700 48.30800 60.51300 scale (grids/A): 2.647365 object centre (A): 8.861502 22.39600 23.96850 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 1.500008 assigned positive charge : 476.2468 centred at (gu) : 92.14435 87.64637 96.08357 assigned negative charge : -474.7480 centred at (gu) : 91.77396 87.88413 96.24277 start vw surface at 0.1300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 183750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25489 grid for indexing accessible points = 1.400000 m= 92661 mr = 136722 m= 31522 mr = 75706 m= 6622 mr = 25190 m= 541 mr = 4678 m= 11 mr = 253 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 3850 time to turn everything in is 1.630000 number of dielectric boundary points 72559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 24470 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) : 1.764910 object centre at (A) : 8.861502 22.39600 23.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8685892 -0.7790168 midg,1,midg; midg,igrid,midg 3.8970385E-02 7.2985545E-02 1,midg,midg; igrid,midg,midg -9.8761454E-02 -2.8738922E-02 gauss-seidel spectral radius is 0.9992215 estimated iterations to convergence 283 setup time was (sec) 1.960000 now iterating at: 14:01:32 rms-change max change #iterations 9.781324 292.6432 at 10iterations 5.600786 111.4270 at 20iterations 3.203181 67.56211 at 30iterations 1.826043 40.20077 at 40iterations 1.038565 20.39185 at 50iterations 0.5909136 10.76119 at 60iterations 0.3356308 6.308798 at 70iterations 0.1906464 3.420497 at 80iterations 0.1080209 2.075832 at 90iterations 6.1370548E-02 1.042904 at 100iterations 3.4864046E-02 0.6256981 at 110iterations 1.9776946E-02 0.3919282 at 120iterations 1.1229970E-02 0.2132645 at 130iterations 6.4090015E-03 0.1091270 at 140iterations 3.6772743E-03 6.9308043E-02 at 150iterations 2.1242227E-03 4.1381836E-02 at 160iterations 1.2442885E-03 2.4139404E-02 at 170iterations 7.4742711E-04 1.6690731E-02 at 180iterations finished qdiffx linear iterations at : 14:01:48 total time elapsed so far: 18.05000 # loops : 180 mean,max change (kT/e) : 7.4742711E-04 1.6690731E-02 energy calculations done at 18.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.22000 DelPhi exited at 14:01:49 18.227u 0.479s 0:19.55 95.6% 0+0k 0+0io 0pf+0w