Tue Oct 11 06:01:53 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 06:01:53 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7565936 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): 25.87800 72.54000 ymin,ymax (A): -18.53100 28.52200 zmin,zma (A): 4.263000 46.49900 x,y,z range (A): 46.66200 47.05300 42.23600 scale (grids/A): 0.7565936 object centre (A): 49.20900 4.995500 25.38100 number of atom coordinates read : 2237 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 89.08775 90.67593 90.15247 assigned negative charge : -304.5422 centred at (gu) : 89.24252 90.54558 90.21362 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8171 nv = 96 ne = 84 npr = 40679 no. pairs analyzed = 40679 no. exposed pairs = 2545 no. arc points = 17564 no. surface atoms = 866 nbur = 1371 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 695 mr = 4831 m= 6 mr = 142 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 0.3000000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1461 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4779771E-07 9.2429509E-08 midg,1,midg; midg,igrid,midg -2.8498772E-09 3.9169589E-07 1,midg,midg; igrid,midg,midg 4.4711226E-07 -3.0741024E-08 gauss-seidel spectral radius is 0.9908829 estimated iterations to convergence 85 setup time was (sec) 0.5500000 now iterating at: 06:01:54 rms-change max change #iterations 0.2644406 33.97845 at 10iterations 3.8526610E-02 5.323995 at 20iterations 5.7222671E-03 0.7276649 at 30iterations 1.0312430E-03 0.1309204 at 40iterations 2.7113897E-04 2.8587341E-02 at 50iterations finished qdiffx linear iterations at : 06:01:56 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 2.7113897E-04 2.8587341E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 06:01:58 3.589u 0.143s 0:04.71 78.9% 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 06:01:58 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.269781 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): 25.87800 72.54000 ymin,ymax (A): -18.53100 28.52200 zmin,zma (A): 4.263000 46.49900 x,y,z range (A): 46.66200 47.05300 42.23600 scale (grids/A): 2.269781 object centre (A): 49.20900 4.995500 25.38100 number of atom coordinates read : 2237 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 87.26330 92.02767 90.45729 assigned negative charge : -304.5422 centred at (gu) : 87.72773 91.63679 90.64098 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 85317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17564 grid for indexing accessible points = 1.400000 m= 37525 mr = 61020 m= 8579 mr = 29158 m= 1010 mr = 5952 m= 39 mr = 565 m= 0 mr = 3 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 35772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15355 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) : 0.7565936 object centre at (A) : 49.20900 4.995500 25.38100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4212707E-02 4.2913955E-02 midg,1,midg; midg,igrid,midg 5.0869267E-02 0.1164198 1,midg,midg; igrid,midg,midg 6.5080792E-02 -7.8182988E-02 gauss-seidel spectral radius is 0.9989563 estimated iterations to convergence 245 setup time was (sec) 1.010000 now iterating at: 06:01:59 rms-change max change #iterations 5.135973 202.9792 at 10iterations 2.649339 83.31161 at 20iterations 1.363896 37.37575 at 30iterations 0.7051302 20.59365 at 40iterations 0.3638937 12.37496 at 50iterations 0.1881247 5.293981 at 60iterations 9.7343713E-02 3.108034 at 70iterations 5.0295345E-02 1.403752 at 80iterations 2.6142487E-02 0.7609787 at 90iterations 1.3684510E-02 0.3830643 at 100iterations 7.1851402E-03 0.2005119 at 110iterations 3.8254824E-03 0.1028519 at 120iterations finished qdiffx linear iterations at : 06:02:06 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 3.8254824E-03 0.1028519 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 06:02:07 8.233u 0.266s 0:09.90 85.7% 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 Tue Oct 11 2011 at 06:02:08 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2237 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.404671 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): 25.87800 72.54000 ymin,ymax (A): -18.53100 28.52200 zmin,zma (A): 4.263000 46.49900 x,y,z range (A): 46.66200 47.05300 42.23600 scale (grids/A): 3.404671 object centre (A): 49.20900 4.995500 25.38100 number of atom coordinates read : 2237 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 311.5670 centred at (gu) : 85.89504 93.04130 90.68589 assigned negative charge : -304.5422 centred at (gu) : 86.59176 92.45524 90.96148 start vw surface at 0.1500000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 196407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17564 grid for indexing accessible points = 1.400000 m= 112472 mr = 146428 m= 50973 mr = 94833 m= 16717 mr = 42689 m= 4056 mr = 13244 m= 601 mr = 3042 m= 40 mr = 405 m= 0 mr = 8 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.260000 number of dielectric boundary points 80617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.420000 number of grid points assigned charge 15416 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) : 2.269781 object centre at (A) : 49.20900 4.995500 25.38100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1170929E-02 0.3098530 midg,1,midg; midg,igrid,midg 0.3659067 0.8129382 1,midg,midg; igrid,midg,midg 0.5544100 -0.8428924 gauss-seidel spectral radius is 0.9993294 estimated iterations to convergence 305 setup time was (sec) 2.610000 now iterating at: 06:02:11 rms-change max change #iterations 11.06379 378.2324 at 10iterations 6.666991 154.0426 at 20iterations 3.991524 88.40674 at 30iterations 2.387253 45.29581 at 40iterations 1.423578 24.16750 at 50iterations 0.8490360 16.08138 at 60iterations 0.5060234 8.816422 at 70iterations 0.3010150 4.990826 at 80iterations 0.1788193 3.516601 at 90iterations 0.1066810 1.672554 at 100iterations 6.3610435E-02 1.192505 at 110iterations 3.8051493E-02 0.6266832 at 120iterations 2.3046311E-02 0.3731155 at 130iterations 1.4190875E-02 0.2516327 at 140iterations 9.0266094E-03 0.1586456 at 150iterations 6.0227308E-03 0.1087570 at 160iterations 4.2325626E-03 8.7474823E-02 at 170iterations 3.1602895E-03 5.9169769E-02 at 180iterations finished qdiffx linear iterations at : 06:02:22 total time elapsed so far: 13.97000 # loops : 180 mean,max change (kT/e) : 3.1602895E-03 5.9169769E-02 energy calculations done at 13.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.17000 DelPhi exited at 06:02:23 14.169u 0.262s 0:15.06 95.7% 0+0k 0+0io 0pf+0w