Sun Oct 9 01:48:44 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 Sun Oct 9 2011 at 01:48:44 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3344 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5725589 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): -16.38300 40.46600 ymin,ymax (A): -10.27600 51.90100 zmin,zma (A): -11.61800 50.47500 x,y,z range (A): 56.84900 62.17700 62.09300 scale (grids/A): 0.5725589 object centre (A): 12.04150 20.81250 19.42850 number of atom coordinates read : 3344 total number of charged atoms : 3201 net assigned charge : 12.45703 assigned positive charge : 496.1956 centred at (gu) : 89.95159 90.48068 89.10293 assigned negative charge : -483.7403 centred at (gu) : 89.80867 90.35453 88.93710 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7564 nv = 96 ne = 84 npr = 64475 no. pairs analyzed = 64475 no. exposed pairs = 4545 no. arc points = 33320 no. surface atoms = 1492 nbur = 1852 mkacc time = 0.1400000 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 = 1.484000 m= 339 mr = 3815 m= 0 mr = 19 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3400000 number of dielectric boundary points 4069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3290 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3156863E-09 4.1713148E-09 midg,1,midg; midg,igrid,midg -2.2899359E-10 4.9700102E-09 1,midg,midg; igrid,midg,midg -6.0029920E-10 4.6852175E-09 gauss-seidel spectral radius is 0.9843042 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 01:48:45 rms-change max change #iterations 9.6914537E-02 14.08517 at 10iterations 7.2908658E-03 1.183611 at 20iterations 5.7850813E-04 8.5960388E-02 at 30iterations 5.0000050E-05 6.7863464E-03 at 40iterations 6.2567528E-06 6.7895651E-04 at 50iterations finished qdiffx linear iterations at : 01:48:48 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 6.2567528E-06 6.7895651E-04 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 01:48:48 3.303u 0.181s 0:03.97 87.6% 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 Sun Oct 9 2011 at 01:48:48 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3344 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 1.717677 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): -16.38300 40.46600 ymin,ymax (A): -10.27600 51.90100 zmin,zma (A): -11.61800 50.47500 x,y,z range (A): 56.84900 62.17700 62.09300 scale (grids/A): 1.717677 object centre (A): 12.04150 20.81250 19.42850 number of atom coordinates read : 3344 total number of charged atoms : 3201 net assigned charge : 12.45703 assigned positive charge : 496.1956 centred at (gu) : 89.85374 91.44140 87.30797 assigned negative charge : -483.7403 centred at (gu) : 89.42567 91.06305 86.81099 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33320 grid for indexing accessible points = 1.400000 m= 27371 mr = 54557 m= 3352 mr = 18905 m= 108 mr = 1683 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1615 time to turn everything in is 0.5800000 number of dielectric boundary points 38003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 325 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 24762 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) : 0.5725589 object centre at (A) : 12.04150 20.81250 19.42850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6411515E-02 5.0707918E-02 midg,1,midg; midg,igrid,midg 9.6747978E-03 5.1478017E-02 1,midg,midg; igrid,midg,midg -8.9650704E-03 1.4978796E-02 gauss-seidel spectral radius is 0.9984227 estimated iterations to convergence 200 setup time was (sec) 0.8800000 now iterating at: 01:48:49 rms-change max change #iterations 3.908145 152.0395 at 10iterations 1.715263 60.25302 at 20iterations 0.7577038 23.62907 at 30iterations 0.3331731 10.35329 at 40iterations 0.1469720 4.760540 at 50iterations 6.5102875E-02 2.150562 at 60iterations 2.8760614E-02 1.099134 at 70iterations 1.2681425E-02 0.4064074 at 80iterations 5.6247693E-03 0.1717329 at 90iterations 2.4949114E-03 7.9463959E-02 at 100iterations 1.0988861E-03 3.7889481E-02 at 110iterations 4.8781073E-04 1.7280579E-02 at 120iterations finished qdiffx linear iterations at : 01:48:56 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 4.8781073E-04 1.7280579E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 01:48:56 7.580u 0.194s 0:08.10 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 Sun Oct 9 2011 at 01:48:57 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3344 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.576515 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): -16.38300 40.46600 ymin,ymax (A): -10.27600 51.90100 zmin,zma (A): -11.61800 50.47500 x,y,z range (A): 56.84900 62.17700 62.09300 scale (grids/A): 2.576515 object centre (A): 12.04150 20.81250 19.42850 number of atom coordinates read : 3344 total number of charged atoms : 3201 net assigned charge : 12.45703 assigned positive charge : 496.1956 centred at (gu) : 89.78039 92.16183 85.96175 assigned negative charge : -483.7403 centred at (gu) : 89.13841 91.59455 85.21632 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 190529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33320 grid for indexing accessible points = 1.400000 m= 91048 mr = 133668 m= 29087 mr = 71468 m= 5485 mr = 22025 m= 478 mr = 3610 m= 9 mr = 208 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 5454 time to turn everything in is 1.420000 number of dielectric boundary points 85657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 25572 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) : 1.717677 object centre at (A) : 12.04150 20.81250 19.42850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1878403 0.8416433 midg,1,midg; midg,igrid,midg 0.2622368 0.7828265 1,midg,midg; igrid,midg,midg -7.5028278E-02 0.2011190 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.740000 now iterating at: 01:48:59 rms-change max change #iterations 9.922044 337.0823 at 10iterations 5.789474 137.9407 at 20iterations 3.358352 81.13350 at 30iterations 1.935138 41.19534 at 40iterations 1.111567 27.96702 at 50iterations 0.6368086 13.32315 at 60iterations 0.3639400 7.314324 at 70iterations 0.2077502 4.473755 at 80iterations 0.1184605 2.225067 at 90iterations 6.7507841E-02 1.326445 at 100iterations 3.8429562E-02 0.7130561 at 110iterations 2.1824060E-02 0.4340487 at 120iterations 1.2455966E-02 0.2285156 at 130iterations 7.0667551E-03 0.1354675 at 140iterations 4.0130313E-03 7.6736450E-02 at 150iterations 2.2827322E-03 3.9810181E-02 at 160iterations 1.2974577E-03 2.4234772E-02 at 170iterations 7.3707936E-04 1.3563156E-02 at 180iterations finished qdiffx linear iterations at : 01:49:12 total time elapsed so far: 14.83000 # loops : 180 mean,max change (kT/e) : 7.3707936E-04 1.3563156E-02 energy calculations done at 14.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.01000 DelPhi exited at 01:49:12 15.009u 0.229s 0:15.56 97.8% 0+0k 0+0io 0pf+0w