Sat Oct 8 15:54:04 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 15:54:04 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2346 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6638942 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): -2.370000 46.83500 ymin,ymax (A): -16.83400 30.04400 zmin,zma (A): -18.75900 34.86400 x,y,z range (A): 49.20500 46.87800 53.62300 scale (grids/A): 0.6638942 object centre (A): 22.23250 6.605000 8.052502 number of atom coordinates read : 2346 total number of charged atoms : 2282 net assigned charge : 3.806002 assigned positive charge : 352.5470 centred at (gu) : 90.71188 88.97469 90.62022 assigned negative charge : -348.7419 centred at (gu) : 90.79794 89.10941 90.66840 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7087 nv = 96 ne = 84 npr = 46420 no. pairs analyzed = 46420 no. exposed pairs = 3042 no. arc points = 21020 no. surface atoms = 1037 nbur = 1309 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3898 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2700000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2073 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7662988E-08 1.2290556E-09 midg,1,midg; midg,igrid,midg 4.5459736E-08 -1.2905518E-08 1,midg,midg; igrid,midg,midg 2.3640606E-08 -7.5215922E-09 gauss-seidel spectral radius is 0.9882200 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 15:54:05 rms-change max change #iterations 0.1607039 24.53320 at 10iterations 1.7132223E-02 2.349533 at 20iterations 1.9314247E-03 0.2803268 at 30iterations 2.5804949E-04 3.6668777E-02 at 40iterations 5.2460269E-05 7.7009201E-03 at 50iterations finished qdiffx linear iterations at : 15:54:09 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 5.2460269E-05 7.7009201E-03 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 15:54:10 4.964u 0.431s 0:05.66 95.2% 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 15:54:10 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2346 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.991683 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): -2.370000 46.83500 ymin,ymax (A): -16.83400 30.04400 zmin,zma (A): -18.75900 34.86400 x,y,z range (A): 49.20500 46.87800 53.62300 scale (grids/A): 1.991683 object centre (A): 22.23250 6.605000 8.052502 number of atom coordinates read : 2346 total number of charged atoms : 2282 net assigned charge : 3.806002 assigned positive charge : 352.5470 centred at (gu) : 92.13494 86.92345 91.86028 assigned negative charge : -348.7419 centred at (gu) : 92.39368 87.32814 92.00535 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21020 grid for indexing accessible points = 1.400000 m= 28517 mr = 53401 m= 5278 mr = 21161 m= 348 mr = 3493 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 666 time to turn everything in is 0.6400000 number of dielectric boundary points 32368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18066 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) : 0.6638942 object centre at (A) : 22.23250 6.605000 8.052502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8638683E-02 4.6789600E-03 midg,1,midg; midg,igrid,midg 2.4517357E-02 -5.8736620E-03 1,midg,midg; igrid,midg,midg 1.1935712E-02 -5.3349670E-02 gauss-seidel spectral radius is 0.9987265 estimated iterations to convergence 222 setup time was (sec) 1.030000 now iterating at: 15:54:11 rms-change max change #iterations 4.410604 218.0374 at 10iterations 2.119929 67.66450 at 20iterations 1.018910 33.29290 at 30iterations 0.4901668 14.92504 at 40iterations 0.2357637 7.415410 at 50iterations 0.1134947 3.922493 at 60iterations 5.4548502E-02 1.659333 at 70iterations 2.6233669E-02 0.8189240 at 80iterations 1.2647357E-02 0.3720279 at 90iterations 6.0850782E-03 0.2114410 at 100iterations 2.9425067E-03 9.3003273E-02 at 110iterations 1.4277529E-03 4.7241211E-02 at 120iterations finished qdiffx linear iterations at : 15:54:23 total time elapsed so far: 12.99000 # loops : 120 mean,max change (kT/e) : 1.4277529E-03 4.7241211E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 15:54:24 13.155u 0.523s 0:13.97 97.8% 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 15:54:24 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2346 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.987524 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): -2.370000 46.83500 ymin,ymax (A): -16.83400 30.04400 zmin,zma (A): -18.75900 34.86400 x,y,z range (A): 49.20500 46.87800 53.62300 scale (grids/A): 2.987524 object centre (A): 22.23250 6.605000 8.052502 number of atom coordinates read : 2346 total number of charged atoms : 2282 net assigned charge : 3.806002 assigned positive charge : 352.5470 centred at (gu) : 93.20242 85.38495 92.79032 assigned negative charge : -348.7419 centred at (gu) : 93.59044 85.99229 93.00805 start vw surface at 0.1100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 176849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21020 grid for indexing accessible points = 1.400000 m= 90873 mr = 129540 m= 35279 mr = 74414 m= 9715 mr = 28601 m= 1529 mr = 7598 m= 84 mr = 1049 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 2027 time to turn everything in is 1.710000 number of dielectric boundary points 73093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 18256 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) : 1.991683 object centre at (A) : 22.23250 6.605000 8.052502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2437670 -5.4192538E-03 midg,1,midg; midg,igrid,midg 0.1351155 -6.4211413E-02 1,midg,midg; igrid,midg,midg 9.2750840E-02 -0.7710677 gauss-seidel spectral radius is 0.9992840 estimated iterations to convergence 295 setup time was (sec) 2.070000 now iterating at: 15:54:27 rms-change max change #iterations 10.14577 386.9733 at 10iterations 5.991684 135.8219 at 20iterations 3.544766 68.00381 at 30iterations 2.087724 42.59553 at 40iterations 1.224087 25.21850 at 50iterations 0.7157736 13.40527 at 60iterations 0.4197056 9.563702 at 70iterations 0.2438812 4.411071 at 80iterations 0.1427080 2.663550 at 90iterations 8.2946584E-02 1.464131 at 100iterations 4.8295736E-02 0.8434176 at 110iterations 2.8071575E-02 0.4739103 at 120iterations 1.6363436E-02 0.2954865 at 130iterations 9.4841551E-03 0.2095814 at 140iterations 5.5075288E-03 9.9764585E-02 at 150iterations 3.2155027E-03 5.5528641E-02 at 160iterations 1.8733469E-03 3.4895897E-02 at 170iterations 1.1005769E-03 1.9601822E-02 at 180iterations finished qdiffx linear iterations at : 15:54:46 total time elapsed so far: 21.55000 # loops : 180 mean,max change (kT/e) : 1.1005769E-03 1.9601822E-02 energy calculations done at 21.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.71000 DelPhi exited at 15:54:47 21.712u 0.507s 0:22.53 98.5% 0+0k 0+0io 0pf+0w