Sat Oct 8 14:08:32 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 8 2011 at 14:08:32 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6319340 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): -11.39600 43.31500 ymin,ymax (A): 10.28200 55.09800 zmin,zma (A): 36.32000 92.65500 x,y,z range (A): 54.71100 44.81600 56.33500 scale (grids/A): 0.6319340 object centre (A): 15.95950 32.69000 64.48750 number of atom coordinates read : 2943 total number of charged atoms : 2797 net assigned charge : -1.999991 assigned positive charge : 440.1437 centred at (gu) : 89.18748 89.65433 91.95234 assigned negative charge : -442.1444 centred at (gu) : 89.17137 89.56764 91.91222 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7930 nv = 96 ne = 84 npr = 61300 no. pairs analyzed = 61300 no. exposed pairs = 3403 no. arc points = 23208 no. surface atoms = 1160 nbur = 1783 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 4690 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2304 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9562 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3420076E-09 3.0212610E-09 midg,1,midg; midg,igrid,midg -1.2506351E-08 6.2564212E-09 1,midg,midg; igrid,midg,midg -4.8089182E-09 -5.4222721E-10 gauss-seidel spectral radius is 0.9870535 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 14:08:33 rms-change max change #iterations 0.1530487 27.27296 at 10iterations 1.5127646E-02 1.897385 at 20iterations 1.5824017E-03 0.2046509 at 30iterations 2.0106223E-04 2.7620316E-02 at 40iterations 3.5211702E-05 5.1794052E-03 at 50iterations finished qdiffx linear iterations at : 14:08:37 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 3.5211702E-05 5.1794052E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 14:08:37 4.236u 0.295s 0:04.81 93.9% 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 Sat Oct 8 2011 at 14:08:37 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.895802 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): -11.39600 43.31500 ymin,ymax (A): 10.28200 55.09800 zmin,zma (A): 36.32000 92.65500 x,y,z range (A): 54.71100 44.81600 56.33500 scale (grids/A): 1.895802 object centre (A): 15.95950 32.69000 64.48750 number of atom coordinates read : 2943 total number of charged atoms : 2797 net assigned charge : -1.999991 assigned positive charge : 440.1437 centred at (gu) : 87.56190 88.96216 95.85686 assigned negative charge : -442.1444 centred at (gu) : 87.51390 88.70234 95.73639 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 32038 mr = 63039 m= 4776 mr = 24387 m= 230 mr = 2917 m= 1 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.7600000 number of dielectric boundary points 33232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21973 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) : 0.6319340 object centre at (A) : 15.95950 32.69000 64.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4610738E-02 -2.3981880E-03 midg,1,midg; midg,igrid,midg -1.8359902E-03 1.2073538E-02 1,midg,midg; igrid,midg,midg -1.4350575E-02 6.5974691E-03 gauss-seidel spectral radius is 0.9986516 estimated iterations to convergence 216 setup time was (sec) 1.060000 now iterating at: 14:08:38 rms-change max change #iterations 4.578700 184.9197 at 10iterations 2.159349 68.00436 at 20iterations 1.018618 30.38069 at 30iterations 0.4777661 14.34516 at 40iterations 0.2261233 7.402260 at 50iterations 0.1065392 3.288162 at 60iterations 5.0163936E-02 1.492257 at 70iterations 2.3637014E-02 0.6918106 at 80iterations 1.1204438E-02 0.3311710 at 90iterations 5.2921218E-03 0.1519489 at 100iterations 2.5050573E-03 7.6309204E-02 at 110iterations 1.1873748E-03 3.6720276E-02 at 120iterations finished qdiffx linear iterations at : 14:08:47 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 1.1873748E-03 3.6720276E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 14:08:48 9.929u 0.344s 0:10.54 97.3% 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 14:08:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.843703 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): -11.39600 43.31500 ymin,ymax (A): 10.28200 55.09800 zmin,zma (A): 36.32000 92.65500 x,y,z range (A): 54.71100 44.81600 56.33500 scale (grids/A): 2.843703 object centre (A): 15.95950 32.69000 64.48750 number of atom coordinates read : 2943 total number of charged atoms : 2797 net assigned charge : -1.999991 assigned positive charge : 440.1437 centred at (gu) : 86.34288 88.44318 98.78518 assigned negative charge : -442.1444 centred at (gu) : 86.27081 88.05341 98.60463 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 200387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 104667 mr = 152051 m= 37501 mr = 87700 m= 8529 mr = 30665 m= 1110 mr = 6254 m= 37 mr = 690 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 406 time to turn everything in is 1.970000 number of dielectric boundary points 74863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 22376 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) : 1.895802 object centre at (A) : 15.95950 32.69000 64.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1345122E-02 4.7854494E-02 midg,1,midg; midg,igrid,midg -1.2517752E-03 0.1622483 1,midg,midg; igrid,midg,midg 3.5310589E-02 0.2682856 gauss-seidel spectral radius is 0.9992665 estimated iterations to convergence 291 setup time was (sec) 2.330000 now iterating at: 14:08:50 rms-change max change #iterations 10.67079 387.5384 at 10iterations 6.280171 143.6044 at 20iterations 3.664381 70.00185 at 30iterations 2.132479 39.87260 at 40iterations 1.237643 29.72562 at 50iterations 0.7167124 13.06387 at 60iterations 0.4157190 7.129326 at 70iterations 0.2403425 4.498308 at 80iterations 0.1388424 2.357872 at 90iterations 8.0300234E-02 1.373493 at 100iterations 4.6388339E-02 0.8314400 at 110iterations 2.6802827E-02 0.4789066 at 120iterations 1.5447646E-02 0.2749233 at 130iterations 8.9376075E-03 0.1572766 at 140iterations 5.1679751E-03 8.5205078E-02 at 150iterations 2.9897911E-03 5.0327778E-02 at 160iterations 1.7383175E-03 2.7538300E-02 at 170iterations 1.0159583E-03 1.7982483E-02 at 180iterations finished qdiffx linear iterations at : 14:09:05 total time elapsed so far: 16.75000 # loops : 180 mean,max change (kT/e) : 1.0159583E-03 1.7982483E-02 energy calculations done at 16.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 14:09:05 16.937u 0.311s 0:17.53 98.3% 0+0k 0+0io 0pf+0w