Sat Oct 8 20:41:31 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 Sat Oct 8 2011 at 20:41:31 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 454 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6158423 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): -31.11700 17.15800 ymin,ymax (A): -23.72100 23.46300 zmin,zma (A): -12.57400 45.23300 x,y,z range (A): 48.27500 47.18400 57.80700 scale (grids/A): 0.6158423 object centre (A): -6.979500 -0.1289997 16.32950 number of atom coordinates read : 2588 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.54401 89.10901 89.67066 assigned negative charge : -387.4045 centred at (gu) : 88.44856 89.15189 89.53690 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6296 nv = 96 ne = 84 npr = 54238 no. pairs analyzed = 54238 no. exposed pairs = 3029 no. arc points = 21406 no. surface atoms = 1022 nbur = 1566 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3478 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.3000000 number of dielectric boundary points 3109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2126 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7938 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4252500E-09 9.8949773E-09 midg,1,midg; midg,igrid,midg 6.6097807E-09 3.5699496E-10 1,midg,midg; igrid,midg,midg -3.8618304E-09 6.1412382E-09 gauss-seidel spectral radius is 0.9863411 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 20:41:32 rms-change max change #iterations 0.1208520 20.38980 at 10iterations 1.1074989E-02 1.675152 at 20iterations 1.0316961E-03 0.1692886 at 30iterations 1.0653640E-04 1.7778397E-02 at 40iterations 1.3935086E-05 3.0031204E-03 at 50iterations finished qdiffx linear iterations at : 20:41:35 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.3935086E-05 3.0031204E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 20:41:35 3.365u 0.180s 0:03.85 91.9% 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 20:41:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 454 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.847527 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): -31.11700 17.15800 ymin,ymax (A): -23.72100 23.46300 zmin,zma (A): -12.57400 45.23300 x,y,z range (A): 48.27500 47.18400 57.80700 scale (grids/A): 1.847527 object centre (A): -6.979500 -0.1289997 16.32950 number of atom coordinates read : 2588 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.63165 87.32668 89.01112 assigned negative charge : -387.4045 centred at (gu) : 85.34557 87.45546 88.61053 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 69378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21406 grid for indexing accessible points = 1.400000 m= 23639 mr = 48578 m= 3250 mr = 17273 m= 121 mr = 1903 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3244 time to turn everything in is 0.4800000 number of dielectric boundary points 28614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19272 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) : 0.6158423 object centre at (A) : -6.979500 -0.1289997 16.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9243753E-02 2.8576026E-02 midg,1,midg; midg,igrid,midg 1.0753031E-02 1.1961522E-04 1,midg,midg; igrid,midg,midg -1.8981772E-03 3.2450628E-02 gauss-seidel spectral radius is 0.9985458 estimated iterations to convergence 208 setup time was (sec) 0.7800000 now iterating at: 20:41:36 rms-change max change #iterations 3.930382 171.9998 at 10iterations 1.804251 61.50072 at 20iterations 0.8198600 30.17686 at 30iterations 0.3747329 15.54721 at 40iterations 0.1719700 5.542526 at 50iterations 7.8550786E-02 2.504206 at 60iterations 3.5880838E-02 1.185771 at 70iterations 1.6387645E-02 0.5033264 at 80iterations 7.4967244E-03 0.2575912 at 90iterations 3.4336180E-03 0.1173897 at 100iterations 1.5751284E-03 4.9798965E-02 at 110iterations 7.2001677E-04 2.5672913E-02 at 120iterations finished qdiffx linear iterations at : 20:41:43 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 7.2001677E-04 2.5672913E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 20:41:43 7.472u 0.233s 0:07.98 96.4% 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 Sat Oct 8 2011 at 20:41:43 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2588 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 454 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.771291 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): -31.11700 17.15800 ymin,ymax (A): -23.72100 23.46300 zmin,zma (A): -12.57400 45.23300 x,y,z range (A): 48.27500 47.18400 57.80700 scale (grids/A): 2.771291 object centre (A): -6.979500 -0.1289997 16.32950 number of atom coordinates read : 2588 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.44723 85.98986 88.51658 assigned negative charge : -387.4045 centred at (gu) : 83.01822 86.18321 87.91560 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 161000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21406 grid for indexing accessible points = 1.400000 m= 78478 mr = 117815 m= 26052 mr = 64221 m= 5479 mr = 20715 m= 517 mr = 3941 m= 14 mr = 286 m= 0 mr = 2 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 10994 time to turn everything in is 1.240000 number of dielectric boundary points 64560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 19631 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) : 1.847527 object centre at (A) : -6.979500 -0.1289997 16.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1161037 0.3327212 midg,1,midg; midg,igrid,midg 0.1281537 -1.3953925E-02 1,midg,midg; igrid,midg,midg -1.2616381E-02 0.4157961 gauss-seidel spectral radius is 0.9992285 estimated iterations to convergence 284 setup time was (sec) 1.550000 now iterating at: 20:41:45 rms-change max change #iterations 9.342632 325.1259 at 10iterations 5.368225 124.5456 at 20iterations 3.064174 65.85229 at 30iterations 1.748762 39.87724 at 40iterations 0.9951608 20.25805 at 50iterations 0.5661867 11.22910 at 60iterations 0.3223275 5.863047 at 70iterations 0.1828140 3.544100 at 80iterations 0.1040464 1.961357 at 90iterations 5.9019573E-02 1.128321 at 100iterations 3.3487767E-02 0.7225933 at 110iterations 1.8999709E-02 0.3554955 at 120iterations 1.0796035E-02 0.2165756 at 130iterations 6.1273254E-03 0.1148119 at 140iterations 3.4794104E-03 6.5546036E-02 at 150iterations 1.9758311E-03 3.8870335E-02 at 160iterations 1.1225764E-03 2.3313522E-02 at 170iterations 6.3645933E-04 1.1314392E-02 at 180iterations finished qdiffx linear iterations at : 20:41:55 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 6.3645933E-04 1.1314392E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 20:41:56 12.066u 0.229s 0:12.56 97.7% 0+0k 0+0io 0pf+0w