Tue Oct 11 06:39:43 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 Tue Oct 11 2011 at 06:39:43 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7115588 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): -20.20200 24.74800 ymin,ymax (A): -28.35900 11.05200 zmin,zma (A): -13.46000 36.57100 x,y,z range (A): 44.95000 39.41100 50.03100 scale (grids/A): 0.7115588 object centre (A): 2.273001 -8.653501 11.55550 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 89.87518 90.60138 89.33961 assigned negative charge : -307.4741 centred at (gu) : 89.68195 90.57361 89.30178 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7053 nv = 96 ne = 84 npr = 41825 no. pairs analyzed = 41825 no. exposed pairs = 2479 no. arc points = 16791 no. surface atoms = 844 nbur = 1221 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4094 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1605 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0267150E-08 7.4980413E-08 midg,1,midg; midg,igrid,midg 4.4769212E-08 8.9239670E-08 1,midg,midg; igrid,midg,midg -4.1415394E-08 1.6203597E-07 gauss-seidel spectral radius is 0.9897001 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:39:44 rms-change max change #iterations 0.2060882 27.90201 at 10iterations 2.6488077E-02 3.855611 at 20iterations 3.5907950E-03 0.4707718 at 30iterations 5.8706570E-04 8.8371277E-02 at 40iterations 1.4434510E-04 2.0534515E-02 at 50iterations finished qdiffx linear iterations at : 06:39:47 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.4434510E-04 2.0534515E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 06:39:47 3.544u 0.193s 0:04.07 91.6% 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 Tue Oct 11 2011 at 06:39:47 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.134676 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): -20.20200 24.74800 ymin,ymax (A): -28.35900 11.05200 zmin,zma (A): -13.46000 36.57100 x,y,z range (A): 44.95000 39.41100 50.03100 scale (grids/A): 2.134676 object centre (A): 2.273001 -8.653501 11.55550 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 89.62564 91.80409 88.01873 assigned negative charge : -307.4741 centred at (gu) : 89.04578 91.72105 87.90547 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16791 grid for indexing accessible points = 1.400000 m= 29898 mr = 53733 m= 5850 mr = 22670 m= 543 mr = 3946 m= 9 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 30709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15343 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) : 0.7115588 object centre at (A) : 2.273001 -8.653501 11.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8341637E-02 4.2786371E-02 midg,1,midg; midg,igrid,midg 4.6153576E-03 3.6529709E-02 1,midg,midg; igrid,midg,midg 1.0059565E-02 4.3931711E-02 gauss-seidel spectral radius is 0.9988394 estimated iterations to convergence 232 setup time was (sec) 0.9000000 now iterating at: 06:39:49 rms-change max change #iterations 4.641258 220.9247 at 10iterations 2.302176 74.92924 at 20iterations 1.147308 35.86649 at 30iterations 0.5703804 17.94797 at 40iterations 0.2847355 8.990501 at 50iterations 0.1424019 4.254063 at 60iterations 7.0777990E-02 2.051888 at 70iterations 3.5384391E-02 1.179543 at 80iterations 1.7748708E-02 0.5750961 at 90iterations 8.9723319E-03 0.2614512 at 100iterations 4.5265849E-03 0.1250610 at 110iterations 2.3446623E-03 7.3669434E-02 at 120iterations finished qdiffx linear iterations at : 06:39:55 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.3446623E-03 7.3669434E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 06:39:56 7.928u 0.199s 0:08.45 95.9% 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 Tue Oct 11 2011 at 06:39:56 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.202015 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): -20.20200 24.74800 ymin,ymax (A): -28.35900 11.05200 zmin,zma (A): -13.46000 36.57100 x,y,z range (A): 44.95000 39.41100 50.03100 scale (grids/A): 3.202015 object centre (A): 2.273001 -8.653501 11.55550 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 89.43858 92.70611 87.02808 assigned negative charge : -307.4741 centred at (gu) : 88.56872 92.58152 86.85820 start vw surface at 0.1300000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 173087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16791 grid for indexing accessible points = 1.400000 m= 93344 mr = 129174 m= 37914 mr = 77797 m= 11262 mr = 31245 m= 2190 mr = 8822 m= 239 mr = 1582 m= 7 mr = 153 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 69269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 15448 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) : 2.134676 object centre at (A) : 2.273001 -8.653501 11.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6217383 0.3528327 midg,1,midg; midg,igrid,midg 1.6470272E-02 0.2895764 1,midg,midg; igrid,midg,midg 0.2243075 0.3270019 gauss-seidel spectral radius is 0.9992931 estimated iterations to convergence 297 setup time was (sec) 2.190000 now iterating at: 06:39:58 rms-change max change #iterations 10.26012 314.5236 at 10iterations 6.073249 118.0194 at 20iterations 3.581475 86.24149 at 30iterations 2.112577 42.74680 at 40iterations 1.242534 23.12644 at 50iterations 0.7289267 14.96332 at 60iterations 0.4282304 9.057003 at 70iterations 0.2508751 4.248213 at 80iterations 0.1471607 2.960355 at 90iterations 8.6144909E-02 1.576330 at 100iterations 5.0680451E-02 1.003016 at 110iterations 2.9901121E-02 0.5247345 at 120iterations 1.7753469E-02 0.3172798 at 130iterations 1.0715009E-02 0.2013736 at 140iterations 6.6470196E-03 0.1204529 at 150iterations 4.2900774E-03 8.2153320E-02 at 160iterations 2.9235065E-03 5.4248810E-02 at 170iterations 2.1106205E-03 3.9375305E-02 at 180iterations finished qdiffx linear iterations at : 06:40:10 total time elapsed so far: 14.18000 # loops : 180 mean,max change (kT/e) : 2.1106205E-03 3.9375305E-02 energy calculations done at 14.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.36000 DelPhi exited at 06:40:11 14.358u 0.233s 0:15.14 96.3% 0+0k 0+0io 0pf+0w