Mon Oct 10 19:33:15 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 19:33:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5981283 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): -25.70600 32.40000 ymin,ymax (A): -11.58100 43.77600 zmin,zma (A): 7.323000 66.84200 x,y,z range (A): 58.10600 55.35700 59.51900 scale (grids/A): 0.5981283 object centre (A): 3.347001 16.09750 37.08250 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271958 assigned positive charge : 478.0415 centred at (gu) : 90.31662 89.44122 91.02962 assigned negative charge : -483.3149 centred at (gu) : 90.38871 89.28513 91.13192 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7598 nv = 96 ne = 84 npr = 63097 no. pairs analyzed = 63097 no. exposed pairs = 4279 no. arc points = 29847 no. surface atoms = 1439 nbur = 1745 mkacc time = 9.9999994E-02 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= 353 mr = 3881 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2300000 number of dielectric boundary points 4050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3009 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8085942E-09 -8.1586942E-09 midg,1,midg; midg,igrid,midg -1.0021985E-08 3.9889358E-09 1,midg,midg; igrid,midg,midg 9.6911212E-10 -5.5037352E-09 gauss-seidel spectral radius is 0.9855919 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 19:33:16 rms-change max change #iterations 0.1177301 15.91181 at 10iterations 9.9318437E-03 1.540121 at 20iterations 8.3662051E-04 0.1061401 at 30iterations 7.2192939E-05 1.0162354E-02 at 40iterations 7.2529506E-06 1.2264252E-03 at 50iterations finished qdiffx linear iterations at : 19:33:19 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.2529506E-06 1.2264252E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:33:20 3.413u 0.169s 0:05.27 67.7% 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 Mon Oct 10 2011 at 19:33:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.794385 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): -25.70600 32.40000 ymin,ymax (A): -11.58100 43.77600 zmin,zma (A): 7.323000 66.84200 x,y,z range (A): 58.10600 55.35700 59.51900 scale (grids/A): 1.794385 object centre (A): 3.347001 16.09750 37.08250 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271958 assigned positive charge : 478.0415 centred at (gu) : 90.94896 88.32293 93.08774 assigned negative charge : -483.3149 centred at (gu) : 91.16565 87.85464 93.39535 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29847 grid for indexing accessible points = 1.400000 m= 27673 mr = 55616 m= 3650 mr = 19154 m= 154 mr = 1920 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 668 time to turn everything in is 0.4100000 number of dielectric boundary points 37603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23760 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) : 0.5981283 object centre at (A) : 3.347001 16.09750 37.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4155551E-03 7.8964951E-03 midg,1,midg; midg,igrid,midg -4.3553900E-02 5.8759777E-03 1,midg,midg; igrid,midg,midg 1.4270801E-02 -4.7647610E-02 gauss-seidel spectral radius is 0.9985313 estimated iterations to convergence 207 setup time was (sec) 0.6300000 now iterating at: 19:33:21 rms-change max change #iterations 4.249291 246.8776 at 10iterations 1.920614 67.22314 at 20iterations 0.8686745 28.05072 at 30iterations 0.3953256 11.97613 at 40iterations 0.1792644 5.370825 at 50iterations 8.1613563E-02 2.874496 at 60iterations 3.7210893E-02 1.288818 at 70iterations 1.6831357E-02 0.5092831 at 80iterations 7.6598558E-03 0.2554555 at 90iterations 3.4909158E-03 0.1183662 at 100iterations 1.5920290E-03 4.6070576E-02 at 110iterations 7.2327611E-04 2.5348663E-02 at 120iterations finished qdiffx linear iterations at : 19:33:29 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 7.2327611E-04 2.5348663E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 19:33:30 8.004u 0.197s 0:08.85 92.5% 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 19:33:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.691577 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): -25.70600 32.40000 ymin,ymax (A): -11.58100 43.77600 zmin,zma (A): 7.323000 66.84200 x,y,z range (A): 58.10600 55.35700 59.51900 scale (grids/A): 2.691577 object centre (A): 3.347001 16.09750 37.08250 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271958 assigned positive charge : 478.0415 centred at (gu) : 91.42316 87.48405 94.63143 assigned negative charge : -483.3149 centred at (gu) : 91.74834 86.78195 95.09303 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29847 grid for indexing accessible points = 1.400000 m= 91314 mr = 135729 m= 30004 mr = 72039 m= 6029 mr = 22976 m= 640 mr = 4058 m= 29 mr = 324 m= 0 mr = 10 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2264 time to turn everything in is 1.040000 number of dielectric boundary points 84867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 24321 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) : 1.794385 object centre at (A) : 3.347001 16.09750 37.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2559377 0.2349354 midg,1,midg; midg,igrid,midg -0.4492260 7.3163763E-02 1,midg,midg; igrid,midg,midg 0.3204961 -0.5159681 gauss-seidel spectral radius is 0.9992555 estimated iterations to convergence 289 setup time was (sec) 1.270000 now iterating at: 19:33:31 rms-change max change #iterations 10.46453 310.6284 at 10iterations 6.192199 157.9104 at 20iterations 3.611186 82.40765 at 30iterations 2.101584 41.15689 at 40iterations 1.217203 22.80737 at 50iterations 0.7033331 12.55029 at 60iterations 0.4058172 7.610436 at 70iterations 0.2341688 4.226271 at 80iterations 0.1345630 2.783067 at 90iterations 7.7425644E-02 1.357197 at 100iterations 4.4451658E-02 0.8132181 at 110iterations 2.5557607E-02 0.4659222 at 120iterations 1.4663467E-02 0.3260880 at 130iterations 8.4371557E-03 0.1669464 at 140iterations 4.8289201E-03 8.4461212E-02 at 150iterations 2.7734186E-03 5.5527687E-02 at 160iterations 1.5939857E-03 2.9504776E-02 at 170iterations 9.1470522E-04 1.8020630E-02 at 180iterations finished qdiffx linear iterations at : 19:33:43 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 9.1470522E-04 1.8020630E-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) 12.91000 DelPhi exited at 19:33:43 12.911u 0.191s 0:13.81 94.8% 0+0k 0+0io 0pf+0w