Sat Oct 15 13:31:02 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 Sat Oct 15 2011 at 13:31:02 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5958059 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 0.5958059 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1998 total number of charged atoms : 1846 net assigned charge : 3.000005 assigned positive charge : 294.0150 centred at (gu) : 90.00063 90.12400 90.42541 assigned negative charge : -291.0153 centred at (gu) : 90.01678 90.21709 90.55592 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4689 nv = 96 ne = 84 npr = 41502 no. pairs analyzed = 41502 no. exposed pairs = 2471 no. arc points = 16844 no. surface atoms = 854 nbur = 1144 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 223 mr = 2587 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1715 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5765 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8367989E-09 -2.2599012E-09 midg,1,midg; midg,igrid,midg 3.2600154E-09 -1.1526328E-09 1,midg,midg; igrid,midg,midg 1.5288171E-09 7.5369733E-10 gauss-seidel spectral radius is 0.9853694 estimated iterations to convergence 68 setup time was (sec) 0.3700000 now iterating at: 13:31:02 rms-change max change #iterations 9.2890367E-02 19.38718 at 10iterations 7.7374931E-03 1.426392 at 20iterations 6.5257977E-04 0.1072483 at 30iterations 5.2748623E-05 9.4852448E-03 at 40iterations 4.4629764E-06 7.3337555E-04 at 50iterations finished qdiffx linear iterations at : 13:31:05 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.4629764E-06 7.3337555E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 13:31:06 3.451u 0.176s 0:03.98 90.9% 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 Sat Oct 15 2011 at 13:31:06 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.787418 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 1.787418 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1998 total number of charged atoms : 1846 net assigned charge : 3.000005 assigned positive charge : 294.0150 centred at (gu) : 90.00169 90.37210 91.27618 assigned negative charge : -291.0153 centred at (gu) : 90.05048 90.65160 91.66804 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 50768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16844 grid for indexing accessible points = 1.400000 m= 17588 mr = 34783 m= 2360 mr = 13197 m= 103 mr = 1427 m= 0 mr = 31 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 442 time to turn everything in is 0.2400000 number of dielectric boundary points 21381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 14430 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) : 0.5958059 object centre at (A) : 4.965502 0.8720007 17.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5299328E-03 -5.2822209E-03 midg,1,midg; midg,igrid,midg 7.1828109E-03 -2.9868330E-03 1,midg,midg; igrid,midg,midg 3.4929235E-02 2.8462807E-02 gauss-seidel spectral radius is 0.9983752 estimated iterations to convergence 197 setup time was (sec) 0.4600000 now iterating at: 13:31:06 rms-change max change #iterations 3.214535 153.0931 at 10iterations 1.402340 52.55965 at 20iterations 0.6139952 24.42041 at 30iterations 0.2669887 10.55605 at 40iterations 0.1165234 4.462423 at 50iterations 5.1091541E-02 1.979622 at 60iterations 2.2325380E-02 0.8386860 at 70iterations 9.7673498E-03 0.3521862 at 80iterations 4.2831860E-03 0.1720781 at 90iterations 1.8697743E-03 7.2116852E-02 at 100iterations 8.1754563E-04 3.3394814E-02 at 110iterations 3.5674300E-04 1.3111115E-02 at 120iterations finished qdiffx linear iterations at : 13:31:14 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 3.5674300E-04 1.3111115E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 13:31:14 7.741u 0.229s 0:08.30 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 Sat Oct 15 2011 at 13:31:14 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.681127 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 2.681127 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1998 total number of charged atoms : 1846 net assigned charge : 3.000005 assigned positive charge : 294.0150 centred at (gu) : 90.00249 90.55812 91.91422 assigned negative charge : -291.0153 centred at (gu) : 90.07569 90.97742 92.50215 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 117286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16844 grid for indexing accessible points = 1.400000 m= 58140 mr = 84288 m= 19981 mr = 47798 m= 4064 mr = 16320 m= 383 mr = 2999 m= 23 mr = 219 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 0.6300000 number of dielectric boundary points 48237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14765 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) : 1.787418 object centre at (A) : 4.965502 0.8720007 17.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6229204E-02 -3.8739797E-02 midg,1,midg; midg,igrid,midg 6.3696600E-02 -3.0562636E-02 1,midg,midg; igrid,midg,midg 0.4193469 0.4312971 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 0.8400000 now iterating at: 13:31:15 rms-change max change #iterations 7.767269 277.7791 at 10iterations 4.381951 123.3534 at 20iterations 2.453726 84.11755 at 30iterations 1.364636 37.64952 at 40iterations 0.7560778 16.96070 at 50iterations 0.4203331 9.432464 at 60iterations 0.2334849 5.157806 at 70iterations 0.1296840 3.173113 at 80iterations 7.1749657E-02 1.598526 at 90iterations 3.9903272E-02 1.020008 at 100iterations 2.2086114E-02 0.4984436 at 110iterations 1.2234072E-02 0.2788239 at 120iterations 6.7810342E-03 0.1488800 at 130iterations 3.7464942E-03 8.8152647E-02 at 140iterations 2.0797483E-03 4.6268463E-02 at 150iterations 1.1527105E-03 2.6069641E-02 at 160iterations 6.3742022E-04 1.3380051E-02 at 170iterations 3.5324291E-04 7.7686310E-03 at 180iterations finished qdiffx linear iterations at : 13:31:26 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 3.5324291E-04 7.7686310E-03 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 13:31:26 11.692u 0.222s 0:12.21 97.5% 0+0k 0+0io 0pf+0w