Tue Oct 11 06:54:01 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 06:54:01 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2501 !!! WARNING: HIQ 106 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6442389 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): -10.65100 44.60800 ymin,ymax (A): 24.43500 79.58300 zmin,zma (A): -70.84200 -27.56500 x,y,z range (A): 55.25900 55.14800 43.27700 scale (grids/A): 0.6442389 object centre (A): 16.97850 52.00900 -49.20350 number of atom coordinates read : 2501 total number of charged atoms : 2363 net assigned charge : -2.485992 assigned positive charge : 360.5372 centred at (gu) : 88.89986 90.14796 89.83661 assigned negative charge : -363.0236 centred at (gu) : 88.99687 90.33025 89.83105 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7201 nv = 96 ne = 84 npr = 50533 no. pairs analyzed = 50533 no. exposed pairs = 3364 no. arc points = 23959 no. surface atoms = 1134 nbur = 1367 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 432 mr = 3769 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8367 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0075499E-09 -3.3672480E-09 midg,1,midg; midg,igrid,midg 1.7132775E-08 -2.7773117E-08 1,midg,midg; igrid,midg,midg 9.7066293E-09 -1.2781042E-08 gauss-seidel spectral radius is 0.9875191 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 06:54:02 rms-change max change #iterations 0.1469274 24.88869 at 10iterations 1.4754535E-02 2.254536 at 20iterations 1.4647844E-03 0.2073021 at 30iterations 1.5018448E-04 2.5085449E-02 at 40iterations 1.6794815E-05 2.5367737E-03 at 50iterations finished qdiffx linear iterations at : 06:54:05 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.6794815E-05 2.5367737E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:54:05 3.402u 0.172s 0:03.88 92.0% 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 06:54:05 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2501 !!! WARNING: HIQ 106 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.932717 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): -10.65100 44.60800 ymin,ymax (A): 24.43500 79.58300 zmin,zma (A): -70.84200 -27.56500 x,y,z range (A): 55.25900 55.14800 43.27700 scale (grids/A): 1.932717 object centre (A): 16.97850 52.00900 -49.20350 number of atom coordinates read : 2501 total number of charged atoms : 2363 net assigned charge : -2.485992 assigned positive charge : 360.5372 centred at (gu) : 86.69904 90.44345 89.50936 assigned negative charge : -363.0236 centred at (gu) : 86.99050 90.99068 89.49286 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23959 grid for indexing accessible points = 1.400000 m= 29156 mr = 51609 m= 5202 mr = 21345 m= 325 mr = 3249 m= 6 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 35130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18636 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) : 0.6442389 object centre at (A) : 16.97850 52.00900 -49.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0829109E-02 1.4859939E-02 midg,1,midg; midg,igrid,midg -8.5561555E-03 -4.6892691E-02 1,midg,midg; igrid,midg,midg -1.2085753E-03 -5.4897308E-02 gauss-seidel spectral radius is 0.9986787 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 06:54:06 rms-change max change #iterations 4.212486 202.7363 at 10iterations 2.003067 65.10132 at 20iterations 0.9501541 31.93151 at 30iterations 0.4515490 14.70340 at 40iterations 0.2140186 7.001851 at 50iterations 0.1017219 3.732496 at 60iterations 4.8242155E-02 1.516000 at 70iterations 2.2886783E-02 0.7921295 at 80iterations 1.0874465E-02 0.3508453 at 90iterations 5.1569897E-03 0.1712151 at 100iterations 2.4441204E-03 8.1222296E-02 at 110iterations 1.1596560E-03 3.4282684E-02 at 120iterations finished qdiffx linear iterations at : 06:54:13 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.1596560E-03 3.4282684E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 06:54:14 7.959u 0.187s 0:08.60 94.5% 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 06:54:14 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2501 !!! WARNING: HIQ 106 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.899075 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): -10.65100 44.60800 ymin,ymax (A): 24.43500 79.58300 zmin,zma (A): -70.84200 -27.56500 x,y,z range (A): 55.25900 55.14800 43.27700 scale (grids/A): 2.899075 object centre (A): 16.97850 52.00900 -49.20350 number of atom coordinates read : 2501 total number of charged atoms : 2363 net assigned charge : -2.485992 assigned positive charge : 360.5372 centred at (gu) : 85.04858 90.66522 89.26383 assigned negative charge : -363.0236 centred at (gu) : 85.48568 91.48603 89.23929 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 176898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23959 grid for indexing accessible points = 1.400000 m= 90868 mr = 125133 m= 36233 mr = 73521 m= 9344 mr = 29162 m= 1351 mr = 6906 m= 91 mr = 867 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 79173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18898 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) : 1.932717 object centre at (A) : 16.97850 52.00900 -49.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1510956 0.2107561 midg,1,midg; midg,igrid,midg -4.5937080E-02 -0.1965993 1,midg,midg; igrid,midg,midg -4.3581292E-02 -1.026905 gauss-seidel spectral radius is 0.9992902 estimated iterations to convergence 296 setup time was (sec) 1.250000 now iterating at: 06:54:15 rms-change max change #iterations 9.914730 396.3812 at 10iterations 5.925227 127.4618 at 20iterations 3.506177 74.93767 at 30iterations 2.064489 44.80197 at 40iterations 1.216833 23.40004 at 50iterations 0.7124184 13.25299 at 60iterations 0.4170659 8.945764 at 70iterations 0.2434982 4.472221 at 80iterations 0.1422194 2.593801 at 90iterations 8.2979783E-02 1.577464 at 100iterations 4.8284646E-02 0.8377604 at 110iterations 2.8113773E-02 0.5277938 at 120iterations 1.6354272E-02 0.2934496 at 130iterations 9.5598390E-03 0.1603289 at 140iterations 5.5527110E-03 9.9806547E-02 at 150iterations 3.2239556E-03 6.8528175E-02 at 160iterations 1.8779075E-03 3.6163330E-02 at 170iterations 1.0931212E-03 2.0912170E-02 at 180iterations finished qdiffx linear iterations at : 06:54:27 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.0931212E-03 2.0912170E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 06:54:27 12.835u 0.211s 0:13.54 96.3% 0+0k 0+0io 0pf+0w