Mon Oct 10 17:04:08 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 17:04:08 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4388 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5123334 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): -16.59900 37.97900 ymin,ymax (A): -33.06500 31.51300 zmin,zma (A): -3.931000 65.55500 x,y,z range (A): 54.57800 64.57800 69.48600 scale (grids/A): 0.5123334 object centre (A): 10.69000 -0.7759991 30.81200 number of atom coordinates read : 4388 total number of charged atoms : 4140 net assigned charge : 3.606023 assigned positive charge : 654.5533 centred at (gu) : 90.06596 91.14070 87.49902 assigned negative charge : -650.9512 centred at (gu) : 89.92189 91.17677 87.51719 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7336 nv = 96 ne = 84 npr = 88833 no. pairs analyzed = 88833 no. exposed pairs = 5720 no. arc points = 39752 no. surface atoms = 1909 nbur = 2479 mkacc time = 0.1900000 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 = 1.652000 m= 296 mr = 3718 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3789 ## 548 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9425396E-10 5.3363889E-12 midg,1,midg; midg,igrid,midg 1.0777668E-10 -5.0921548E-11 1,midg,midg; igrid,midg,midg -3.0997097E-10 4.1801718E-10 gauss-seidel spectral radius is 0.9804916 estimated iterations to convergence 59 setup time was (sec) 0.6400000 now iterating at: 17:04:09 rms-change max change #iterations 6.7638718E-02 11.13845 at 10iterations 3.9636390E-03 0.6382217 at 20iterations 4.3450185E-04 6.8405151E-02 at 30iterations 1.3417001E-04 1.8407822E-02 at 40iterations 4.8248381E-05 6.7405701E-03 at 50iterations finished qdiffx linear iterations at : 17:04:12 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 4.8248381E-05 6.7405701E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 17:04:13 3.200u 0.151s 0:04.21 79.5% 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 17:04:13 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4388 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.537000 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): -16.59900 37.97900 ymin,ymax (A): -33.06500 31.51300 zmin,zma (A): -3.931000 65.55500 x,y,z range (A): 54.57800 64.57800 69.48600 scale (grids/A): 1.537000 object centre (A): 10.69000 -0.7759991 30.81200 number of atom coordinates read : 4388 total number of charged atoms : 4140 net assigned charge : 3.606023 assigned positive charge : 654.5533 centred at (gu) : 90.19675 93.42108 82.49573 assigned negative charge : -650.9512 centred at (gu) : 89.76553 93.53017 82.55128 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 83348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39752 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23955 mr = 56718 m= 2048 mr = 15622 m= 46 mr = 796 m= 0 mr = 4 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 239 time to turn everything in is 0.5800000 number of dielectric boundary points 36257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 533 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 31134 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) : 0.5123334 object centre at (A) : 10.69000 -0.7759991 30.81200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4832183E-03 7.9845758E-03 midg,1,midg; midg,igrid,midg -2.2362173E-03 -1.3638083E-02 1,midg,midg; igrid,midg,midg -5.0977296E-03 9.2908423E-03 gauss-seidel spectral radius is 0.9980916 estimated iterations to convergence 182 setup time was (sec) 0.8400000 now iterating at: 17:04:14 rms-change max change #iterations 3.658709 164.4025 at 10iterations 1.488302 53.02666 at 20iterations 0.6057814 21.53514 at 30iterations 0.2468590 9.444069 at 40iterations 0.1005858 3.949013 at 50iterations 4.1122578E-02 1.310665 at 60iterations 1.6771656E-02 0.5853424 at 70iterations 6.9130091E-03 0.2365179 at 80iterations 2.8580686E-03 9.2044830E-02 at 90iterations 1.2049656E-03 3.8419008E-02 at 100iterations 5.3473562E-04 1.8692970E-02 at 110iterations 2.6105795E-04 8.3446503E-03 at 120iterations finished qdiffx linear iterations at : 17:04:20 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 2.6105795E-04 8.3446503E-03 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 17:04:21 7.010u 0.180s 0:08.72 82.4% 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 17:04:22 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4388 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.305500 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): -16.59900 37.97900 ymin,ymax (A): -33.06500 31.51300 zmin,zma (A): -3.931000 65.55500 x,y,z range (A): 54.57800 64.57800 69.48600 scale (grids/A): 2.305500 object centre (A): 10.69000 -0.7759991 30.81200 number of atom coordinates read : 4388 total number of charged atoms : 4140 net assigned charge : 3.606023 assigned positive charge : 654.5533 centred at (gu) : 90.29473 95.13142 78.74307 assigned negative charge : -650.9512 centred at (gu) : 89.64830 95.29510 78.82681 start vw surface at 0.2000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 194205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39752 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86348 mr = 139779 m= 21294 mr = 66608 m= 2927 mr = 14975 m= 169 mr = 1731 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 797 time to turn everything in is 1.350000 number of dielectric boundary points 81800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 33026 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) : 1.537000 object centre at (A) : 10.69000 -0.7759991 30.81200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1844004 0.2281048 midg,1,midg; midg,igrid,midg -9.0400361E-02 -0.3583889 1,midg,midg; igrid,midg,midg -6.6720404E-02 0.1221096 gauss-seidel spectral radius is 0.9991491 estimated iterations to convergence 271 setup time was (sec) 1.630000 now iterating at: 17:04:23 rms-change max change #iterations 9.874006 329.8743 at 10iterations 5.650944 166.8536 at 20iterations 3.200953 69.32184 at 30iterations 1.798032 40.56712 at 40iterations 1.011524 21.93226 at 50iterations 0.5646730 13.11298 at 60iterations 0.3158379 7.437237 at 70iterations 0.1756025 3.840879 at 80iterations 9.7861864E-02 1.990635 at 90iterations 5.4156587E-02 1.230637 at 100iterations 3.0116297E-02 0.6730957 at 110iterations 1.6666200E-02 0.3423729 at 120iterations 9.2320517E-03 0.1794090 at 130iterations 5.1201535E-03 0.1074104 at 140iterations 2.8326523E-03 5.6283951E-02 at 150iterations 1.5719605E-03 3.2592773E-02 at 160iterations 8.7025051E-04 1.7202377E-02 at 170iterations 4.8411405E-04 1.0454178E-02 at 180iterations finished qdiffx linear iterations at : 17:04:33 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 4.8411405E-04 1.0454178E-02 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 17:04:34 11.224u 0.178s 0:12.05 94.5% 0+0k 0+0io 0pf+0w