Mon Oct 10 17:04:42 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 17:04:42 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 = 3184 !!! WARNING: HIR 148 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6029402 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): -9.146000 47.86500 ymin,ymax (A): -8.753000 46.23600 zmin,zma (A): -3.936000 55.10800 x,y,z range (A): 57.01100 54.98900 59.04400 scale (grids/A): 0.6029402 object centre (A): 19.35950 18.74150 25.58600 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -3.985958 assigned positive charge : 482.6336 centred at (gu) : 89.65234 87.87884 88.99958 assigned negative charge : -486.6209 centred at (gu) : 89.60515 87.77220 88.90840 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7672 nv = 96 ne = 84 npr = 64403 no. pairs analyzed = 64403 no. exposed pairs = 4176 no. arc points = 29281 no. surface atoms = 1408 nbur = 1776 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3968 m= 4 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3600000 number of dielectric boundary points 4057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2967 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8615656E-09 2.2202036E-09 midg,1,midg; midg,igrid,midg -1.1478899E-08 2.1731983E-09 1,midg,midg; igrid,midg,midg -4.3631907E-09 6.0222421E-10 gauss-seidel spectral radius is 0.9858152 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 17:04:43 rms-change max change #iterations 0.1236635 20.15467 at 10iterations 1.0409032E-02 1.616391 at 20iterations 9.0534659E-04 0.1397285 at 30iterations 8.0346268E-05 1.2201309E-02 at 40iterations 8.2084225E-06 1.2063980E-03 at 50iterations finished qdiffx linear iterations at : 17:04:46 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.2084225E-06 1.2063980E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:04:47 3.603u 0.210s 0:04.55 83.7% 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 17:04:47 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 = 3184 !!! WARNING: HIR 148 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.808821 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): -9.146000 47.86500 ymin,ymax (A): -8.753000 46.23600 zmin,zma (A): -3.936000 55.10800 x,y,z range (A): 57.01100 54.98900 59.04400 scale (grids/A): 1.808821 object centre (A): 19.35950 18.74150 25.58600 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -3.985958 assigned positive charge : 482.6336 centred at (gu) : 88.95594 83.63555 86.99824 assigned negative charge : -486.6209 centred at (gu) : 88.81499 83.31623 86.72508 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 83290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29281 grid for indexing accessible points = 1.400000 m= 26874 mr = 56163 m= 3358 mr = 18454 m= 151 mr = 1792 m= 4 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 0.6300000 number of dielectric boundary points 37237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23761 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) : 0.6029402 object centre at (A) : 19.35950 18.74150 25.58600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8807838E-03 7.0703928E-03 midg,1,midg; midg,igrid,midg -3.3486988E-02 4.6094349E-03 1,midg,midg; igrid,midg,midg -4.3553520E-02 8.1662741E-03 gauss-seidel spectral radius is 0.9985468 estimated iterations to convergence 208 setup time was (sec) 0.9200000 now iterating at: 17:04:48 rms-change max change #iterations 4.347430 192.2918 at 10iterations 1.978495 74.71593 at 20iterations 0.8999974 28.40224 at 30iterations 0.4112139 13.05602 at 40iterations 0.1879584 6.416206 at 50iterations 8.5870318E-02 2.572790 at 60iterations 3.9164402E-02 1.278937 at 70iterations 1.7912949E-02 0.5794096 at 80iterations 8.1807533E-03 0.2481108 at 90iterations 3.7391027E-03 0.1200714 at 100iterations 1.7023121E-03 4.9288273E-02 at 110iterations 7.8039721E-04 2.4455070E-02 at 120iterations finished qdiffx linear iterations at : 17:04:55 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 7.8039721E-04 2.4455070E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:04:56 7.643u 0.177s 0:08.80 88.7% 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 17:04:56 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 = 3184 !!! WARNING: HIR 148 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.713231 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): -9.146000 47.86500 ymin,ymax (A): -8.753000 46.23600 zmin,zma (A): -3.936000 55.10800 x,y,z range (A): 57.01100 54.98900 59.04400 scale (grids/A): 2.713231 object centre (A): 19.35950 18.74150 25.58600 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -3.985958 assigned positive charge : 482.6336 centred at (gu) : 88.43374 80.45317 85.49717 assigned negative charge : -486.6209 centred at (gu) : 88.22242 79.97424 85.08754 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 193303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29281 grid for indexing accessible points = 1.400000 m= 90184 mr = 137329 m= 28600 mr = 71068 m= 5648 mr = 21751 m= 560 mr = 3773 m= 19 mr = 313 m= 0 mr = 3 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1796 time to turn everything in is 1.530000 number of dielectric boundary points 84077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 24327 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) : 1.808821 object centre at (A) : 19.35950 18.74150 25.58600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2128970 -2.9171869E-02 midg,1,midg; midg,igrid,midg -0.3308118 6.1638433E-02 1,midg,midg; igrid,midg,midg -0.4698829 0.1768972 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.850000 now iterating at: 17:04:58 rms-change max change #iterations 10.51613 328.6367 at 10iterations 6.180948 158.9273 at 20iterations 3.597320 70.88740 at 30iterations 2.090277 45.19211 at 40iterations 1.207763 24.11141 at 50iterations 0.6965970 15.07467 at 60iterations 0.4023092 7.296043 at 70iterations 0.2311765 4.368496 at 80iterations 0.1329782 2.479631 at 90iterations 7.6598771E-02 1.607773 at 100iterations 4.3990247E-02 0.7917824 at 110iterations 2.5277687E-02 0.4625468 at 120iterations 1.4526225E-02 0.2500365 at 130iterations 8.3460342E-03 0.1448383 at 140iterations 4.7869501E-03 8.6112976E-02 at 150iterations 2.7442456E-03 4.9732208E-02 at 160iterations 1.5790657E-03 2.7036399E-02 at 170iterations 9.0593932E-04 1.5366554E-02 at 180iterations finished qdiffx linear iterations at : 17:05:08 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 9.0593932E-04 1.5366554E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 17:05:10 12.509u 0.225s 0:13.64 93.2% 0+0k 0+0io 0pf+0w