Sat Oct 8 11:37:46 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 8 2011 at 11:37:46 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4669 !!! WARNING: HIT 440 has a net charge of 0.5140 !!! WARNING: ALA 536 has a net charge of -0.2720 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: 0.5537839 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): -27.24900 35.12900 ymin,ymax (A): 33.77600 98.06100 zmin,zma (A): 30.58900 89.96600 x,y,z range (A): 62.37800 64.28500 59.37700 scale (grids/A): 0.5537839 object centre (A): 3.939999 65.91850 60.27750 number of atom coordinates read : 4669 total number of charged atoms : 4506 net assigned charge : -7.757962 assigned positive charge : 706.9545 centred at (gu) : 90.61509 88.91972 88.97169 assigned negative charge : -714.7162 centred at (gu) : 90.51968 88.95402 89.12543 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8957 nv = 96 ne = 84 npr = 98184 no. pairs analyzed = 98184 no. exposed pairs = 5280 no. arc points = 35884 no. surface atoms = 1803 nbur = 2866 mkacc time = 0.1600000 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 = 1.540000 m= 370 mr = 5121 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.3200000 number of dielectric boundary points 4186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3740 ## 496 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 12093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8921720E-09 -2.2687106E-09 midg,1,midg; midg,igrid,midg -2.5616065E-10 -9.0918312E-10 1,midg,midg; igrid,midg,midg -1.7746112E-09 7.6473866E-10 gauss-seidel spectral radius is 0.9833001 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 11:37:46 rms-change max change #iterations 0.1018136 13.93732 at 10iterations 7.6329885E-03 0.9834343 at 20iterations 8.1106770E-04 0.1124954 at 30iterations 1.9384827E-04 2.5309563E-02 at 40iterations 6.5271728E-05 9.3936920E-03 at 50iterations finished qdiffx linear iterations at : 11:37:49 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 6.5271728E-05 9.3936920E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 11:37:50 3.599u 0.180s 0:04.07 92.6% 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 Sat Oct 8 2011 at 11:37:50 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4669 !!! WARNING: HIT 440 has a net charge of 0.5140 !!! WARNING: ALA 536 has a net charge of -0.2720 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: 1.661352 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): -27.24900 35.12900 ymin,ymax (A): 33.77600 98.06100 zmin,zma (A): 30.58900 89.96600 x,y,z range (A): 62.37800 64.28500 59.37700 scale (grids/A): 1.661352 object centre (A): 3.939999 65.91850 60.27750 number of atom coordinates read : 4669 total number of charged atoms : 4506 net assigned charge : -7.757962 assigned positive charge : 706.9545 centred at (gu) : 91.84409 86.75826 86.91376 assigned negative charge : -714.7162 centred at (gu) : 91.55859 86.86169 87.37591 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 101691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35884 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32914 mr = 73609 m= 3703 mr = 23896 m= 126 mr = 2089 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5573 time to turn everything in is 0.4900000 number of dielectric boundary points 38822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 401 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 34665 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) : 0.5537839 object centre at (A) : 3.939999 65.91850 60.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2449672E-04 -2.8081192E-02 midg,1,midg; midg,igrid,midg 1.5618751E-02 -1.2056243E-03 1,midg,midg; igrid,midg,midg -1.3659210E-02 1.6033735E-02 gauss-seidel spectral radius is 0.9983924 estimated iterations to convergence 198 setup time was (sec) 0.7200000 now iterating at: 11:37:51 rms-change max change #iterations 4.502870 155.7865 at 10iterations 1.977721 59.31171 at 20iterations 0.8727843 27.94902 at 30iterations 0.3836811 10.97445 at 40iterations 0.1686220 4.952637 at 50iterations 7.4256003E-02 2.179981 at 60iterations 3.2651581E-02 0.9316265 at 70iterations 1.4432694E-02 0.3718262 at 80iterations 6.4233346E-03 0.1879234 at 90iterations 2.8770163E-03 8.0721855E-02 at 100iterations 1.3218359E-03 4.0523767E-02 at 110iterations 6.2861049E-04 2.0460933E-02 at 120iterations finished qdiffx linear iterations at : 11:37:58 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 6.2861049E-04 2.0460933E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 11:37:59 8.206u 0.199s 0:08.91 94.1% 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 Sat Oct 8 2011 at 11:37:59 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4669 !!! WARNING: HIT 440 has a net charge of 0.5140 !!! WARNING: ALA 536 has a net charge of -0.2720 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: 2.492028 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): -27.24900 35.12900 ymin,ymax (A): 33.77600 98.06100 zmin,zma (A): 30.58900 89.96600 x,y,z range (A): 62.37800 64.28500 59.37700 scale (grids/A): 2.492028 object centre (A): 3.939999 65.91850 60.27750 number of atom coordinates read : 4669 total number of charged atoms : 4506 net assigned charge : -7.757962 assigned positive charge : 706.9545 centred at (gu) : 92.76565 85.13709 85.37041 assigned negative charge : -714.7162 centred at (gu) : 92.33774 85.29230 86.06380 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 236798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35884 grid for indexing accessible points = 1.400000 m= 114064 mr = 179178 m= 33889 mr = 93492 m= 6143 mr = 26438 m= 507 mr = 4412 m= 6 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 18406 time to turn everything in is 1.200000 number of dielectric boundary points 87620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 36011 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) : 1.661352 object centre at (A) : 3.939999 65.91850 60.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1002260E-02 -0.3549201 midg,1,midg; midg,igrid,midg 0.3597475 -1.5037042E-03 1,midg,midg; igrid,midg,midg -0.1815044 0.1627651 gauss-seidel spectral radius is 0.9992219 estimated iterations to convergence 283 setup time was (sec) 1.460000 now iterating at: 11:38:01 rms-change max change #iterations 11.47918 298.8959 at 10iterations 6.625641 128.4016 at 20iterations 3.824753 75.86928 at 30iterations 2.188858 37.34256 at 40iterations 1.252778 23.59363 at 50iterations 0.7145289 11.39910 at 60iterations 0.4075963 6.852265 at 70iterations 0.2319180 4.051041 at 80iterations 0.1319955 2.258207 at 90iterations 7.4998654E-02 1.290788 at 100iterations 4.2606208E-02 0.7338600 at 110iterations 2.4259033E-02 0.4032059 at 120iterations 1.3790628E-02 0.2595253 at 130iterations 7.9127848E-03 0.1482792 at 140iterations 4.5592226E-03 7.6116562E-02 at 150iterations 2.6692864E-03 5.3466797E-02 at 160iterations 1.6066523E-03 2.6802063E-02 at 170iterations 1.0004719E-03 1.8995285E-02 at 180iterations finished qdiffx linear iterations at : 11:38:13 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 1.0004719E-03 1.8995285E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 11:38:13 13.635u 0.235s 0:14.41 96.1% 0+0k 0+0io 0pf+0w