Mon Oct 10 23:16:16 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 Mon Oct 10 2011 at 23:16:16 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 0.6360323 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): -19.88900 30.63300 ymin,ymax (A): 17.59000 73.56200 zmin,zma (A): 9.662001 51.86300 x,y,z range (A): 50.52200 55.97200 42.20100 scale (grids/A): 0.6360323 object centre (A): 5.372000 45.57600 30.76250 number of atom coordinates read : 2647 total number of charged atoms : 2502 net assigned charge : 5.406024 assigned positive charge : 398.6397 centred at (gu) : 91.57951 90.09673 89.84555 assigned negative charge : -393.2344 centred at (gu) : 91.58342 90.32322 90.04292 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7017 nv = 96 ne = 84 npr = 53893 no. pairs analyzed = 53893 no. exposed pairs = 3083 no. arc points = 21470 no. surface atoms = 1048 nbur = 1599 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 4000 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.2900000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2054 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8502 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8411355E-08 -1.3791071E-08 midg,1,midg; midg,igrid,midg 2.9787447E-08 -1.7892157E-08 1,midg,midg; igrid,midg,midg 5.3869731E-09 9.2324379E-09 gauss-seidel spectral radius is 0.9871937 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 23:16:17 rms-change max change #iterations 0.1484205 21.24795 at 10iterations 1.4719551E-02 2.090782 at 20iterations 2.0348143E-03 0.3935318 at 30iterations 4.9425417E-04 0.1167603 at 40iterations 1.5873824E-04 3.8406372E-02 at 50iterations finished qdiffx linear iterations at : 23:16:20 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.5873824E-04 3.8406372E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 23:16:20 3.286u 0.194s 0:04.05 85.6% 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 Mon Oct 10 2011 at 23:16:20 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.908097 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): -19.88900 30.63300 ymin,ymax (A): 17.59000 73.56200 zmin,zma (A): 9.662001 51.86300 x,y,z range (A): 50.52200 55.97200 42.20100 scale (grids/A): 1.908097 object centre (A): 5.372000 45.57600 30.76250 number of atom coordinates read : 2647 total number of charged atoms : 2502 net assigned charge : 5.406024 assigned positive charge : 398.6397 centred at (gu) : 94.73797 90.28959 89.53631 assigned negative charge : -393.2344 centred at (gu) : 94.74982 90.96928 90.12865 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21470 grid for indexing accessible points = 1.400000 m= 27389 mr = 54240 m= 4207 mr = 20459 m= 247 mr = 2829 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 4682 time to turn everything in is 0.5200000 number of dielectric boundary points 30821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19683 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) : 0.6360323 object centre at (A) : 5.372000 45.57600 30.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7264150E-02 3.8645756E-03 midg,1,midg; midg,igrid,midg -1.5181758E-02 -2.7444415E-02 1,midg,midg; igrid,midg,midg 1.8672135E-02 3.0303228E-04 gauss-seidel spectral radius is 0.9986378 estimated iterations to convergence 215 setup time was (sec) 0.8200000 now iterating at: 23:16:21 rms-change max change #iterations 4.260680 184.5561 at 10iterations 1.988221 63.06524 at 20iterations 0.9333081 28.17833 at 30iterations 0.4388691 13.69413 at 40iterations 0.2057377 6.414333 at 50iterations 9.6291825E-02 3.062431 at 60iterations 4.5288760E-02 1.536777 at 70iterations 2.1483114E-02 0.6486282 at 80iterations 1.0179117E-02 0.3070946 at 90iterations 4.8508588E-03 0.1626816 at 100iterations 2.3811560E-03 9.4204903E-02 at 110iterations 1.2265979E-03 4.5146942E-02 at 120iterations finished qdiffx linear iterations at : 23:16:28 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 1.2265979E-03 4.5146942E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 23:16:29 7.432u 0.209s 0:08.16 93.5% 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 Mon Oct 10 2011 at 23:16:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2647 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 2.862145 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): -19.88900 30.63300 ymin,ymax (A): 17.59000 73.56200 zmin,zma (A): 9.662001 51.86300 x,y,z range (A): 50.52200 55.97200 42.20100 scale (grids/A): 2.862145 object centre (A): 5.372000 45.57600 30.76250 number of atom coordinates read : 2647 total number of charged atoms : 2502 net assigned charge : 5.406024 assigned positive charge : 398.6397 centred at (gu) : 97.10683 90.43436 89.30427 assigned negative charge : -393.2344 centred at (gu) : 97.12469 91.45382 90.19289 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 177632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21470 grid for indexing accessible points = 1.400000 m= 89086 mr = 131270 m= 31699 mr = 73857 m= 7688 mr = 25856 m= 1031 mr = 5956 m= 42 mr = 733 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 15572 time to turn everything in is 1.340000 number of dielectric boundary points 69499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 20016 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) : 1.908097 object centre at (A) : 5.372000 45.57600 30.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3454078 9.1725476E-02 midg,1,midg; midg,igrid,midg -0.5917203 -0.2541684 1,midg,midg; igrid,midg,midg 0.1656858 -2.0368788E-02 gauss-seidel spectral radius is 0.9992542 estimated iterations to convergence 289 setup time was (sec) 1.650000 now iterating at: 23:16:30 rms-change max change #iterations 9.912940 436.3071 at 10iterations 5.711796 134.3248 at 20iterations 3.285198 59.60415 at 30iterations 1.888200 34.43383 at 40iterations 1.086347 20.04591 at 50iterations 0.6215749 11.62092 at 60iterations 0.3568621 6.148510 at 70iterations 0.2045134 4.082707 at 80iterations 0.1173057 2.054161 at 90iterations 6.7268796E-02 1.172924 at 100iterations 3.8541611E-02 0.7244549 at 110iterations 2.2139082E-02 0.3794785 at 120iterations 1.2738409E-02 0.2280407 at 130iterations 7.3342589E-03 0.1355133 at 140iterations 4.2483634E-03 8.2420349E-02 at 150iterations 2.4842499E-03 4.4231415E-02 at 160iterations 1.4826631E-03 3.1389236E-02 at 170iterations 9.1726548E-04 2.0515442E-02 at 180iterations finished qdiffx linear iterations at : 23:16:41 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 9.1726548E-04 2.0515442E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 23:16:41 12.108u 0.236s 0:12.64 97.5% 0+0k 0+0io 0pf+0w