Mon Oct 10 14:03:28 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 14:03:28 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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: 0.7159808 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): -25.12000 22.03700 ymin,ymax (A): -23.83400 25.88800 zmin,zma (A): -14.29700 35.40200 x,y,z range (A): 47.15700 49.72200 49.69900 scale (grids/A): 0.7159808 object centre (A): -1.541499 1.027000 10.55250 number of atom coordinates read : 2011 total number of charged atoms : 1865 net assigned charge : -0.5689769 assigned positive charge : 303.4279 centred at (gu) : 90.30796 89.74335 90.13497 assigned negative charge : -303.9971 centred at (gu) : 90.18780 89.75691 90.20573 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7093 nv = 96 ne = 84 npr = 41688 no. pairs analyzed = 41688 no. exposed pairs = 2472 no. arc points = 17830 no. surface atoms = 838 nbur = 1173 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 3966 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2800000 number of dielectric boundary points 3522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1559 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3955253E-08 -4.8736393E-08 midg,1,midg; midg,igrid,midg 1.9970630E-09 -1.3235722E-08 1,midg,midg; igrid,midg,midg -7.2248440E-08 6.7080741E-08 gauss-seidel spectral radius is 0.9898297 estimated iterations to convergence 81 setup time was (sec) 0.5000000 now iterating at: 14:03:29 rms-change max change #iterations 0.2113087 28.75074 at 10iterations 2.6451878E-02 3.579445 at 20iterations 3.3514004E-03 0.4739609 at 30iterations 4.1772786E-04 5.6613922E-02 at 40iterations 5.2644697E-05 7.3890686E-03 at 50iterations finished qdiffx linear iterations at : 14:03:32 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 5.2644697E-05 7.3890686E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:03:32 3.113u 0.188s 0:03.81 86.3% 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 Mon Oct 10 2011 at 14:03:32 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.147943 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): -25.12000 22.03700 ymin,ymax (A): -23.83400 25.88800 zmin,zma (A): -14.29700 35.40200 x,y,z range (A): 47.15700 49.72200 49.69900 scale (grids/A): 2.147943 object centre (A): -1.541499 1.027000 10.55250 number of atom coordinates read : 2011 total number of charged atoms : 1865 net assigned charge : -0.5689769 assigned positive charge : 303.4279 centred at (gu) : 90.92388 89.23013 90.40471 assigned negative charge : -303.9971 centred at (gu) : 90.56342 89.27071 90.61710 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17830 grid for indexing accessible points = 1.400000 m= 30072 mr = 51634 m= 6475 mr = 23020 m= 557 mr = 4456 m= 16 mr = 256 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.6000000 number of dielectric boundary points 32248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14822 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) : 0.7159808 object centre at (A) : -1.541499 1.027000 10.55250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0906823E-03 -6.1170768E-02 midg,1,midg; midg,igrid,midg -3.8665071E-02 1.2260562E-02 1,midg,midg; igrid,midg,midg 3.6634463E-03 3.6334131E-02 gauss-seidel spectral radius is 0.9988570 estimated iterations to convergence 234 setup time was (sec) 0.8800000 now iterating at: 14:03:34 rms-change max change #iterations 4.754151 212.9399 at 10iterations 2.358802 86.17308 at 20iterations 1.181090 36.51214 at 30iterations 0.5868942 19.48055 at 40iterations 0.2934612 9.473102 at 50iterations 0.1468867 4.342099 at 60iterations 7.3317274E-02 2.387104 at 70iterations 3.6564454E-02 1.123943 at 80iterations 1.8285520E-02 0.6205292 at 90iterations 9.1306344E-03 0.3407898 at 100iterations 4.5497711E-03 0.1338348 at 110iterations 2.2797110E-03 6.9095612E-02 at 120iterations finished qdiffx linear iterations at : 14:03:40 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 2.2797110E-03 6.9095612E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:03:41 7.655u 0.250s 0:08.31 95.0% 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 14:03:41 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.221914 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): -25.12000 22.03700 ymin,ymax (A): -23.83400 25.88800 zmin,zma (A): -14.29700 35.40200 x,y,z range (A): 47.15700 49.72200 49.69900 scale (grids/A): 3.221914 object centre (A): -1.541499 1.027000 10.55250 number of atom coordinates read : 2011 total number of charged atoms : 1865 net assigned charge : -0.5689769 assigned positive charge : 303.4279 centred at (gu) : 91.38580 88.84513 90.60715 assigned negative charge : -303.9971 centred at (gu) : 90.84515 88.90610 90.92569 start vw surface at 0.1900000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 171758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17830 grid for indexing accessible points = 1.400000 m= 92593 mr = 124528 m= 39756 mr = 77130 m= 12375 mr = 33185 m= 2456 mr = 9736 m= 258 mr = 1752 m= 14 mr = 143 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 1.850000 number of dielectric boundary points 72732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 14920 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) : 2.147943 object centre at (A) : -1.541499 1.027000 10.55250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5691759E-02 -0.5363249 midg,1,midg; midg,igrid,midg -0.5624106 0.2258711 1,midg,midg; igrid,midg,midg 3.7461843E-02 0.1903022 gauss-seidel spectral radius is 0.9993078 estimated iterations to convergence 300 setup time was (sec) 2.160000 now iterating at: 14:03:43 rms-change max change #iterations 10.52623 419.9096 at 10iterations 6.166086 119.8179 at 20iterations 3.618320 74.25573 at 30iterations 2.120111 37.86348 at 40iterations 1.244381 22.89417 at 50iterations 0.7286463 16.43274 at 60iterations 0.4256479 7.053092 at 70iterations 0.2493652 4.720779 at 80iterations 0.1456373 2.389269 at 90iterations 8.5294902E-02 1.538132 at 100iterations 4.9825683E-02 0.8510714 at 110iterations 2.9093599E-02 0.4963226 at 120iterations 1.7027209E-02 0.2878280 at 130iterations 9.9468343E-03 0.1740646 at 140iterations 5.8196760E-03 0.1011214 at 150iterations 3.4018743E-03 6.3027382E-02 at 160iterations 1.9857637E-03 3.5118103E-02 at 170iterations 1.1637879E-03 1.9756317E-02 at 180iterations finished qdiffx linear iterations at : 14:03:54 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 1.1637879E-03 1.9756317E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 14:03:54 12.976u 0.227s 0:13.62 96.8% 0+0k 0+0io 0pf+0w