Sun Oct 9 01:11:33 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 Sun Oct 9 2011 at 01:11:33 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: HIT 84 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6461214 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): -26.76200 26.64700 ymin,ymax (A): 7.932000 51.75500 zmin,zma (A): -13.82400 41.27400 x,y,z range (A): 53.40900 43.82300 55.09800 scale (grids/A): 0.6461214 object centre (A): -5.7498932E-02 29.84350 13.72500 number of atom coordinates read : 2262 total number of charged atoms : 2127 net assigned charge : 10.51403 assigned positive charge : 331.7017 centred at (gu) : 90.57072 90.26932 91.52640 assigned negative charge : -321.1882 centred at (gu) : 90.53706 90.19859 91.56873 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6437 nv = 96 ne = 84 npr = 45174 no. pairs analyzed = 45174 no. exposed pairs = 3056 no. arc points = 22298 no. surface atoms = 1004 nbur = 1258 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3297 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.3500000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2127 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6811335E-08 1.8213479E-08 midg,1,midg; midg,igrid,midg 9.5965609E-09 2.7693993E-08 1,midg,midg; igrid,midg,midg 1.2815629E-08 2.4784706E-08 gauss-seidel spectral radius is 0.9875686 estimated iterations to convergence 73 setup time was (sec) 0.7100000 now iterating at: 01:11:34 rms-change max change #iterations 0.1410875 20.25650 at 10iterations 1.3957123E-02 2.184077 at 20iterations 1.3801609E-03 0.2060127 at 30iterations 1.4471541E-04 2.2315979E-02 at 40iterations 1.5854677E-05 2.3460388E-03 at 50iterations finished qdiffx linear iterations at : 01:11:38 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.5854677E-05 2.3460388E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.850000 DelPhi exited at 01:11:39 4.859u 0.455s 0:05.57 95.1% 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 Sun Oct 9 2011 at 01:11:39 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: HIT 84 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.938364 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): -26.76200 26.64700 ymin,ymax (A): 7.932000 51.75500 zmin,zma (A): -13.82400 41.27400 x,y,z range (A): 53.40900 43.82300 55.09800 scale (grids/A): 1.938364 object centre (A): -5.7498932E-02 29.84350 13.72500 number of atom coordinates read : 2262 total number of charged atoms : 2127 net assigned charge : 10.51403 assigned positive charge : 331.7017 centred at (gu) : 91.71179 90.80779 94.57896 assigned negative charge : -321.1882 centred at (gu) : 91.61142 90.59576 94.70635 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 68842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 24285 mr = 45114 m= 4266 mr = 17321 m= 342 mr = 2654 m= 3 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2680 time to turn everything in is 0.7200000 number of dielectric boundary points 32503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 16737 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) : 0.6461214 object centre at (A) : -5.7498932E-02 29.84350 13.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5424316E-02 2.6573846E-02 midg,1,midg; midg,igrid,midg -3.0753312E-03 2.2672847E-02 1,midg,midg; igrid,midg,midg 4.8423570E-02 6.0024187E-02 gauss-seidel spectral radius is 0.9986599 estimated iterations to convergence 216 setup time was (sec) 1.070000 now iterating at: 01:11:41 rms-change max change #iterations 3.974541 180.6849 at 10iterations 1.864383 63.81950 at 20iterations 0.8802622 31.88762 at 30iterations 0.4123425 13.50874 at 40iterations 0.1938438 6.485381 at 50iterations 9.1156110E-02 3.083036 at 60iterations 4.2995196E-02 1.446039 at 70iterations 2.0185554E-02 0.6907053 at 80iterations 9.4848601E-03 0.3304753 at 90iterations 4.4717104E-03 0.1436920 at 100iterations 2.1002959E-03 8.0677032E-02 at 110iterations 9.9397998E-04 3.3361673E-02 at 120iterations finished qdiffx linear iterations at : 01:11:51 total time elapsed so far: 11.18000 # loops : 120 mean,max change (kT/e) : 9.9397998E-04 3.3361673E-02 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 01:11:51 11.401u 0.485s 0:12.17 97.6% 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 Sun Oct 9 2011 at 01:11:51 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: HIT 84 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.907547 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): -26.76200 26.64700 ymin,ymax (A): 7.932000 51.75500 zmin,zma (A): -13.82400 41.27400 x,y,z range (A): 53.40900 43.82300 55.09800 scale (grids/A): 2.907547 object centre (A): -5.7498932E-02 29.84350 13.72500 number of atom coordinates read : 2262 total number of charged atoms : 2127 net assigned charge : 10.51403 assigned positive charge : 331.7017 centred at (gu) : 92.56756 91.21173 96.86838 assigned negative charge : -321.1882 centred at (gu) : 92.41724 90.89375 97.05962 start vw surface at 0.1500000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 158810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 77818 mr = 109930 m= 29028 mr = 62031 m= 7776 mr = 22965 m= 1402 mr = 5736 m= 103 mr = 944 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 9050 time to turn everything in is 1.880000 number of dielectric boundary points 73280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 17016 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) : 1.938364 object centre at (A) : -5.7498932E-02 29.84350 13.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6480282 0.3152685 midg,1,midg; midg,igrid,midg -3.2038506E-02 0.2168106 1,midg,midg; igrid,midg,midg 0.5495205 0.5755837 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 2.270000 now iterating at: 01:11:54 rms-change max change #iterations 9.483975 436.0689 at 10iterations 5.597222 137.1211 at 20iterations 3.273494 72.49874 at 30iterations 1.909397 40.25659 at 40iterations 1.112056 20.61890 at 50iterations 0.6463103 12.53613 at 60iterations 0.3747330 7.463238 at 70iterations 0.2177055 4.527543 at 80iterations 0.1258386 2.266176 at 90iterations 7.2995655E-02 1.364804 at 100iterations 4.2215209E-02 0.8539467 at 110iterations 2.4401205E-02 0.5178175 at 120iterations 1.4108120E-02 0.2852612 at 130iterations 8.1265699E-03 0.1547089 at 140iterations 4.6962765E-03 8.8215828E-02 at 150iterations 2.7150873E-03 5.2802086E-02 at 160iterations 1.5685088E-03 2.9891968E-02 at 170iterations 9.0301246E-04 1.7477989E-02 at 180iterations finished qdiffx linear iterations at : 01:12:11 total time elapsed so far: 19.36000 # loops : 180 mean,max change (kT/e) : 9.0301246E-04 1.7477989E-02 energy calculations done at 19.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.58000 DelPhi exited at 01:12:12 19.583u 0.517s 0:20.37 98.6% 0+0k 0+0io 0pf+0w