Tue Oct 11 08:34:17 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 Tue Oct 11 2011 at 08:34:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 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: 0.6599926 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): -8.665999 45.27400 ymin,ymax (A): -15.90400 31.24800 zmin,zma (A): -10.28400 43.19100 x,y,z range (A): 53.94000 47.15200 53.47500 scale (grids/A): 0.6599926 object centre (A): 18.30400 7.672001 16.45350 number of atom coordinates read : 2705 total number of charged atoms : 2561 net assigned charge : 4.500014 assigned positive charge : 408.6826 centred at (gu) : 89.67470 89.78738 89.21860 assigned negative charge : -404.1833 centred at (gu) : 89.81448 89.68340 89.26119 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7971 nv = 96 ne = 84 npr = 54532 no. pairs analyzed = 54532 no. exposed pairs = 3247 no. arc points = 22468 no. surface atoms = 1098 nbur = 1607 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4547 m= 0 mr = 84 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.2900000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2095 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9251 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3589944E-08 2.2289754E-09 midg,1,midg; midg,igrid,midg -1.0829032E-08 3.1116365E-08 1,midg,midg; igrid,midg,midg 4.2506056E-08 -1.6653365E-08 gauss-seidel spectral radius is 0.9881103 estimated iterations to convergence 75 setup time was (sec) 0.4900000 now iterating at: 08:34:18 rms-change max change #iterations 0.1738201 26.24182 at 10iterations 1.9039050E-02 2.398344 at 20iterations 2.7594848E-03 0.5243797 at 30iterations 7.0350367E-04 0.1496582 at 40iterations 2.3637792E-04 5.1216125E-02 at 50iterations finished qdiffx linear iterations at : 08:34:20 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 2.3637792E-04 5.1216125E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 08:34:21 3.076u 0.153s 0:03.91 82.3% 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 08:34:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 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: 1.979978 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): -8.665999 45.27400 ymin,ymax (A): -15.90400 31.24800 zmin,zma (A): -10.28400 43.19100 x,y,z range (A): 53.94000 47.15200 53.47500 scale (grids/A): 1.979978 object centre (A): 18.30400 7.672001 16.45350 number of atom coordinates read : 2705 total number of charged atoms : 2561 net assigned charge : 4.500014 assigned positive charge : 408.6826 centred at (gu) : 89.02337 89.36145 87.65491 assigned negative charge : -404.1833 centred at (gu) : 89.44327 89.04994 87.78310 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22468 grid for indexing accessible points = 1.400000 m= 32333 mr = 60790 m= 5666 mr = 24500 m= 393 mr = 3831 m= 4 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4972 time to turn everything in is 0.5900000 number of dielectric boundary points 35113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20237 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) : 0.6599926 object centre at (A) : 18.30400 7.672001 16.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1525881E-02 5.3792777E-03 midg,1,midg; midg,igrid,midg 1.4303179E-02 2.0153811E-02 1,midg,midg; igrid,midg,midg 5.7342160E-02 -3.2721110E-02 gauss-seidel spectral radius is 0.9987400 estimated iterations to convergence 223 setup time was (sec) 0.8500000 now iterating at: 08:34:22 rms-change max change #iterations 4.689583 179.3023 at 10iterations 2.267038 71.27477 at 20iterations 1.092471 33.58291 at 30iterations 0.5263330 15.59443 at 40iterations 0.2540813 7.297745 at 50iterations 0.1228099 3.800261 at 60iterations 5.9436370E-02 1.773445 at 70iterations 2.8842846E-02 0.8301392 at 80iterations 1.4165586E-02 0.4171056 at 90iterations 6.9736312E-03 0.2036743 at 100iterations 3.5276820E-03 0.1131134 at 110iterations 1.8717600E-03 6.4472198E-02 at 120iterations finished qdiffx linear iterations at : 08:34:28 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 1.8717600E-03 6.4472198E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 08:34:29 7.217u 0.175s 0:07.76 95.1% 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 Tue Oct 11 2011 at 08:34:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 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: 2.969967 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): -8.665999 45.27400 ymin,ymax (A): -15.90400 31.24800 zmin,zma (A): -10.28400 43.19100 x,y,z range (A): 53.94000 47.15200 53.47500 scale (grids/A): 2.969967 object centre (A): 18.30400 7.672001 16.45350 number of atom coordinates read : 2705 total number of charged atoms : 2561 net assigned charge : 4.500014 assigned positive charge : 408.6826 centred at (gu) : 88.53487 89.04202 86.48229 assigned negative charge : -404.1833 centred at (gu) : 89.16486 88.57480 86.67464 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 198553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22468 grid for indexing accessible points = 1.400000 m= 103498 mr = 146564 m= 39529 mr = 86169 m= 10606 mr = 32523 m= 1767 mr = 8341 m= 102 mr = 1278 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 17486 time to turn everything in is 1.470000 number of dielectric boundary points 79147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 20487 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) : 1.979978 object centre at (A) : 18.30400 7.672001 16.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2758247 -0.1181947 midg,1,midg; midg,igrid,midg 0.2902426 0.1804071 1,midg,midg; igrid,midg,midg 0.7970150 -0.4432489 gauss-seidel spectral radius is 0.9992790 estimated iterations to convergence 294 setup time was (sec) 1.750000 now iterating at: 08:34:31 rms-change max change #iterations 10.74821 390.8185 at 10iterations 6.268192 126.6203 at 20iterations 3.653753 76.49533 at 30iterations 2.122166 38.03867 at 40iterations 1.232492 22.97965 at 50iterations 0.7158375 13.02127 at 60iterations 0.4157174 7.438971 at 70iterations 0.2406441 4.007101 at 80iterations 0.1397526 2.374783 at 90iterations 8.0848031E-02 1.401878 at 100iterations 4.6941694E-02 0.8147583 at 110iterations 2.7251860E-02 0.4687014 at 120iterations 1.5883423E-02 0.2831688 at 130iterations 9.3330219E-03 0.1762466 at 140iterations 5.5711367E-03 0.1056900 at 150iterations 3.3943912E-03 8.5704803E-02 at 160iterations 2.1437800E-03 4.8358917E-02 at 170iterations 1.4376079E-03 3.3256531E-02 at 180iterations finished qdiffx linear iterations at : 08:34:40 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 1.4376079E-03 3.3256531E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 08:34:41 11.285u 0.165s 0:11.91 96.0% 0+0k 0+0io 0pf+0w