Sat Oct 8 11:39:11 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 Sat Oct 8 2011 at 11:39:11 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIT 134 has a net charge of 0.5140 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: 0.4975889 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): -17.23100 29.82900 ymin,ymax (A): -30.20800 41.33700 zmin,zma (A): -14.74200 51.07800 x,y,z range (A): 47.06000 71.54500 65.82000 scale (grids/A): 0.4975889 object centre (A): 6.299001 5.564499 18.16800 number of atom coordinates read : 3514 total number of charged atoms : 3351 net assigned charge : -3.985976 assigned positive charge : 524.5947 centred at (gu) : 89.91077 90.68436 91.61935 assigned negative charge : -528.5825 centred at (gu) : 89.81320 90.70814 91.65389 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5667 nv = 96 ne = 84 npr = 66798 no. pairs analyzed = 66798 no. exposed pairs = 5231 no. arc points = 38191 no. surface atoms = 1749 nbur = 1765 mkacc time = 0.1100000 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 = 1.708000 m= 187 mr = 2379 m= 0 mr = 1 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3670 ## 602 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2133402E-12 -1.0483989E-10 midg,1,midg; midg,igrid,midg -3.8724974E-12 -6.7096016E-11 1,midg,midg; igrid,midg,midg -1.4027968E-10 7.2199968E-11 gauss-seidel spectral radius is 0.9792843 estimated iterations to convergence 58 setup time was (sec) 0.4400000 now iterating at: 11:39:11 rms-change max change #iterations 4.9465366E-02 9.212086 at 10iterations 2.4862872E-03 0.4467216 at 20iterations 1.6638859E-04 3.3946991E-02 at 30iterations 2.5618321E-05 5.8403015E-03 at 40iterations 5.5457008E-06 1.2884140E-03 at 50iterations finished qdiffx linear iterations at : 11:39:14 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.5457008E-06 1.2884140E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 11:39:15 3.572u 0.181s 0:04.03 93.0% 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 Sat Oct 8 2011 at 11:39:15 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIT 134 has a net charge of 0.5140 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: 1.492767 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): -17.23100 29.82900 ymin,ymax (A): -30.20800 41.33700 zmin,zma (A): -14.74200 51.07800 x,y,z range (A): 47.06000 71.54500 65.82000 scale (grids/A): 1.492767 object centre (A): 6.299001 5.564499 18.16800 number of atom coordinates read : 3514 total number of charged atoms : 3351 net assigned charge : -3.985976 assigned positive charge : 524.5947 centred at (gu) : 89.73127 92.05186 94.85714 assigned negative charge : -528.5825 centred at (gu) : 89.43890 92.12410 94.96135 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15423 mr = 37876 m= 1082 mr = 8971 m= 17 mr = 292 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 32393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 526 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 24983 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) : 0.4975889 object centre at (A) : 6.299001 5.564499 18.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5065890E-05 -4.4308412E-03 midg,1,midg; midg,igrid,midg -9.4115874E-03 -3.7700643E-03 1,midg,midg; igrid,midg,midg -3.4052776E-03 3.3734710E-04 gauss-seidel spectral radius is 0.9978953 estimated iterations to convergence 173 setup time was (sec) 0.5400000 now iterating at: 11:39:16 rms-change max change #iterations 2.962417 147.3163 at 10iterations 1.151187 47.19421 at 20iterations 0.4446104 19.34473 at 30iterations 0.1725980 6.664618 at 40iterations 6.6967584E-02 2.508286 at 50iterations 2.6040062E-02 1.069406 at 60iterations 1.0113827E-02 0.3688250 at 70iterations 3.9461870E-03 0.1579185 at 80iterations 1.5317171E-03 5.7834625E-02 at 90iterations 6.0281291E-04 2.3132324E-02 at 100iterations 2.3727270E-04 9.0332031E-03 at 110iterations 9.4614079E-05 3.8146973E-03 at 120iterations finished qdiffx linear iterations at : 11:39:23 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 9.4614079E-05 3.8146973E-03 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 11:39:23 8.009u 0.229s 0:08.60 95.5% 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 Sat Oct 8 2011 at 11:39:23 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIT 134 has a net charge of 0.5140 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: 2.239150 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): -17.23100 29.82900 ymin,ymax (A): -30.20800 41.33700 zmin,zma (A): -14.74200 51.07800 x,y,z range (A): 47.06000 71.54500 65.82000 scale (grids/A): 2.239150 object centre (A): 6.299001 5.564499 18.16800 number of atom coordinates read : 3514 total number of charged atoms : 3351 net assigned charge : -3.985976 assigned positive charge : 524.5947 centred at (gu) : 89.59674 93.07758 97.28536 assigned negative charge : -528.5825 centred at (gu) : 89.15831 93.18590 97.44196 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 146549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38191 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 56786 mr = 94700 m= 12339 mr = 40436 m= 1305 mr = 7992 m= 46 mr = 622 m= 0 mr = 3 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 73272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 26710 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) : 1.492767 object centre at (A) : 6.299001 5.564499 18.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3681193E-02 2.1715466E-02 midg,1,midg; midg,igrid,midg -0.2408506 -6.3430734E-02 1,midg,midg; igrid,midg,midg -5.3379383E-02 9.4718300E-03 gauss-seidel spectral radius is 0.9990705 estimated iterations to convergence 259 setup time was (sec) 0.9800000 now iterating at: 11:39:25 rms-change max change #iterations 8.290502 238.6014 at 10iterations 4.632327 124.1970 at 20iterations 2.563926 64.47382 at 30iterations 1.406583 35.30334 at 40iterations 0.7690051 20.04844 at 50iterations 0.4193102 11.57352 at 60iterations 0.2275562 5.464890 at 70iterations 0.1234500 3.169143 at 80iterations 6.6698581E-02 1.508485 at 90iterations 3.6031485E-02 0.8298111 at 100iterations 1.9460101E-02 0.4800034 at 110iterations 1.0461243E-02 0.2324486 at 120iterations 5.6466283E-03 0.1460915 at 130iterations 3.0287444E-03 6.5418243E-02 at 140iterations 1.6324588E-03 3.7094116E-02 at 150iterations 8.7802630E-04 1.8681467E-02 at 160iterations 4.7191008E-04 1.0690689E-02 at 170iterations 2.5370831E-04 5.2719116E-03 at 180iterations finished qdiffx linear iterations at : 11:39:36 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 2.5370831E-04 5.2719116E-03 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 11:39:37 12.917u 0.219s 0:13.53 96.9% 0+0k 0+0io 0pf+0w