Mon Oct 10 13:59:41 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 13:59:41 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3269 !!! WARNING: SEP 61 has a net charge of -0.4750 !!! WARNING: GLM 117 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6138777 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): -1.012000 56.98000 ymin,ymax (A): -23.53200 29.97000 zmin,zma (A): -10.79700 44.21400 x,y,z range (A): 57.99200 53.50200 55.01100 scale (grids/A): 0.6138777 object centre (A): 27.98400 3.219000 16.70850 number of atom coordinates read : 3269 total number of charged atoms : 3116 net assigned charge : 3.431008 assigned positive charge : 488.4828 centred at (gu) : 92.23787 88.36059 90.40028 assigned negative charge : -485.0532 centred at (gu) : 92.23470 88.33189 90.46948 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8108 nv = 96 ne = 84 npr = 67339 no. pairs analyzed = 67339 no. exposed pairs = 3748 no. arc points = 26364 no. surface atoms = 1273 nbur = 1996 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 4614 m= 0 mr = 32 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4200000 number of dielectric boundary points 3842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2685 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10095 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4437935E-09 -2.7249332E-09 midg,1,midg; midg,igrid,midg 4.3015441E-10 2.9986229E-09 1,midg,midg; igrid,midg,midg 1.3110624E-09 4.1423829E-09 gauss-seidel spectral radius is 0.9863124 estimated iterations to convergence 70 setup time was (sec) 0.7200000 now iterating at: 13:59:42 rms-change max change #iterations 0.1348739 19.68830 at 10iterations 1.2463486E-02 1.637496 at 20iterations 1.1988867E-03 0.1503067 at 30iterations 1.3929409E-04 1.7511368E-02 at 40iterations 2.4532983E-05 3.7090182E-03 at 50iterations finished qdiffx linear iterations at : 13:59:45 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 2.4532983E-05 3.7090182E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 13:59:46 4.285u 0.244s 0:05.31 85.1% 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 Mon Oct 10 2011 at 13:59:46 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3269 !!! WARNING: SEP 61 has a net charge of -0.4750 !!! WARNING: GLM 117 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.841633 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): -1.012000 56.98000 ymin,ymax (A): -23.53200 29.97000 zmin,zma (A): -10.79700 44.21400 x,y,z range (A): 57.99200 53.50200 55.01100 scale (grids/A): 1.841633 object centre (A): 27.98400 3.219000 16.70850 number of atom coordinates read : 3269 total number of charged atoms : 3116 net assigned charge : 3.431008 assigned positive charge : 488.4828 centred at (gu) : 96.71249 85.08067 91.20034 assigned negative charge : -485.0532 centred at (gu) : 96.70395 84.99505 91.40785 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 88765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26364 grid for indexing accessible points = 1.400000 m= 31302 mr = 63033 m= 4244 mr = 23342 m= 180 mr = 2597 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 864 time to turn everything in is 0.7800000 number of dielectric boundary points 35472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 24413 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) : 0.6138777 object centre at (A) : 27.98400 3.219000 16.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1991281E-02 -3.9073046E-02 midg,1,midg; midg,igrid,midg 1.0290240E-02 1.1566951E-02 1,midg,midg; igrid,midg,midg 3.2524288E-02 3.4789085E-02 gauss-seidel spectral radius is 0.9985991 estimated iterations to convergence 212 setup time was (sec) 1.110000 now iterating at: 13:59:48 rms-change max change #iterations 4.491690 166.7470 at 10iterations 2.080669 64.61031 at 20iterations 0.9675553 31.40125 at 30iterations 0.4477162 13.71041 at 40iterations 0.2083137 6.181593 at 50iterations 9.6574038E-02 2.671798 at 60iterations 4.4879545E-02 1.456239 at 70iterations 2.0788336E-02 0.6626778 at 80iterations 9.7053805E-03 0.2906723 at 90iterations 4.4937143E-03 0.1314812 at 100iterations 2.0924169E-03 5.8181763E-02 at 110iterations 9.7274157E-04 3.2310486E-02 at 120iterations finished qdiffx linear iterations at : 13:59:56 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 9.7274157E-04 3.2310486E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 13:59:57 9.644u 0.275s 0:10.44 94.9% 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 Mon Oct 10 2011 at 13:59:57 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3269 !!! WARNING: SEP 61 has a net charge of -0.4750 !!! WARNING: GLM 117 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.762450 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): -1.012000 56.98000 ymin,ymax (A): -23.53200 29.97000 zmin,zma (A): -10.79700 44.21400 x,y,z range (A): 57.99200 53.50200 55.01100 scale (grids/A): 2.762450 object centre (A): 27.98400 3.219000 16.70850 number of atom coordinates read : 3269 total number of charged atoms : 3116 net assigned charge : 3.431008 assigned positive charge : 488.4828 centred at (gu) : 100.0686 82.62083 91.80026 assigned negative charge : -485.0532 centred at (gu) : 100.0558 82.49251 92.11179 start vw surface at 0.1900000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 205551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26364 grid for indexing accessible points = 1.400000 m= 103723 mr = 152803 m= 35264 mr = 85417 m= 7247 mr = 28523 m= 770 mr = 5347 m= 33 mr = 463 m= 0 mr = 7 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 2937 time to turn everything in is 1.810000 number of dielectric boundary points 80028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 24921 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) : 1.841633 object centre at (A) : 27.98400 3.219000 16.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3053761 -0.4176067 midg,1,midg; midg,igrid,midg 6.2851086E-02 9.9781454E-02 1,midg,midg; igrid,midg,midg 0.3477718 0.4628161 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 2.160000 now iterating at: 13:59:59 rms-change max change #iterations 10.63690 284.1808 at 10iterations 6.231874 128.3760 at 20iterations 3.624394 66.36787 at 30iterations 2.097093 37.57413 at 40iterations 1.213509 25.52323 at 50iterations 0.7015625 11.89594 at 60iterations 0.4041502 6.978379 at 70iterations 0.2330410 3.793499 at 80iterations 0.1345101 2.412676 at 90iterations 7.7355333E-02 1.385178 at 100iterations 4.4528559E-02 0.7573948 at 110iterations 2.5643695E-02 0.4252129 at 120iterations 1.4783446E-02 0.2491622 at 130iterations 8.5051991E-03 0.1388068 at 140iterations 4.9028406E-03 9.3189240E-02 at 150iterations 2.8287130E-03 4.9253464E-02 at 160iterations 1.6352320E-03 2.7559251E-02 at 170iterations 9.4724144E-04 1.5496254E-02 at 180iterations finished qdiffx linear iterations at : 14:00:13 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 9.4724144E-04 1.5496254E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.73000 DelPhi exited at 14:00:14 15.732u 0.275s 0:16.62 96.2% 0+0k 0+0io 0pf+0w