Wed Dec 28 11:02:58 PST 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 Wed Dec 28 2011 at 11:02:58 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 = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 0.5793705 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): -25.72600 35.72000 ymin,ymax (A): -19.06400 20.59400 zmin,zma (A): -3.488000 38.48700 x,y,z range (A): 61.44600 39.65800 41.97500 scale (grids/A): 0.5793705 object centre (A): 4.997001 0.7650003 17.49950 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.4744 centred at (gu) : 89.91444 90.24051 90.57885 assigned negative charge : -289.4262 centred at (gu) : 89.91146 90.34232 90.72813 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4445 nv = 96 ne = 84 npr = 40386 no. pairs analyzed = 40386 no. exposed pairs = 2397 no. arc points = 17156 no. surface atoms = 813 nbur = 1151 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 = 1.512000 m= 171 mr = 2401 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3100000 number of dielectric boundary points 2204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1711 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 5384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3060100E-09 -7.7834708E-09 midg,1,midg; midg,igrid,midg -3.0924689E-09 -6.4687371E-09 1,midg,midg; igrid,midg,midg -4.8080464E-09 -4.5430295E-09 gauss-seidel spectral radius is 0.9845399 estimated iterations to convergence 66 setup time was (sec) 0.7500000 now iterating at: 11:02:59 rms-change max change #iterations 8.3379515E-02 16.04112 at 10iterations 6.4816964E-03 1.277544 at 20iterations 5.0808408E-04 8.9242935E-02 at 30iterations 3.9044164E-05 7.9193115E-03 at 40iterations 3.0549597E-06 5.4550171E-04 at 50iterations finished qdiffx linear iterations at : 11:03:05 total time elapsed so far: 6.150000 # loops : 50 mean,max change (kT/e) : 3.0549597E-06 5.4550171E-04 energy calculations done at 6.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.370000 DelPhi exited at 11:03:05 6.378u 0.643s 0:07.44 94.2% 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 Wed Dec 28 2011 at 11:03:05 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 = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 1.738111 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): -25.72600 35.72000 ymin,ymax (A): -19.06400 20.59400 zmin,zma (A): -3.488000 38.48700 x,y,z range (A): 61.44600 39.65800 41.97500 scale (grids/A): 1.738111 object centre (A): 4.997001 0.7650003 17.49950 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.4744 centred at (gu) : 89.74372 90.72173 91.73660 assigned negative charge : -289.4262 centred at (gu) : 89.73457 91.02706 92.18446 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 48344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17156 grid for indexing accessible points = 1.400000 m= 16292 mr = 33102 m= 1806 mr = 12092 m= 51 mr = 961 m= 0 mr = 8 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 956 time to turn everything in is 0.5400000 number of dielectric boundary points 20330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13762 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) : 0.5793705 object centre at (A) : 4.997001 0.7650003 17.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6290327E-03 -2.7304366E-02 midg,1,midg; midg,igrid,midg -1.0508326E-02 -2.1650063E-02 1,midg,midg; igrid,midg,midg -2.7683038E-02 -3.1780262E-02 gauss-seidel spectral radius is 0.9982838 estimated iterations to convergence 192 setup time was (sec) 1.010000 now iterating at: 11:03:07 rms-change max change #iterations 2.995287 131.9438 at 10iterations 1.277897 52.09167 at 20iterations 0.5451273 24.63660 at 30iterations 0.2325855 8.731798 at 40iterations 9.9213228E-02 4.217855 at 50iterations 4.2619351E-02 1.639503 at 60iterations 1.7994080E-02 0.7402368 at 70iterations 7.7482373E-03 0.3008013 at 80iterations 3.2935841E-03 0.1330214 at 90iterations 1.4134095E-03 6.0131073E-02 at 100iterations 6.0096150E-04 2.3307800E-02 at 110iterations 2.5775330E-04 1.0156631E-02 at 120iterations finished qdiffx linear iterations at : 11:03:21 total time elapsed so far: 15.39000 # loops : 120 mean,max change (kT/e) : 2.5775330E-04 1.0156631E-02 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.61000 DelPhi exited at 11:03:22 15.614u 0.722s 0:16.65 98.0% 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 Wed Dec 28 2011 at 11:03:22 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 = 1964 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 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: 2.607167 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): -25.72600 35.72000 ymin,ymax (A): -19.06400 20.59400 zmin,zma (A): -3.488000 38.48700 x,y,z range (A): 61.44600 39.65800 41.97500 scale (grids/A): 2.607167 object centre (A): 4.997001 0.7650003 17.49950 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.4744 centred at (gu) : 89.61571 91.08263 92.60500 assigned negative charge : -289.4262 centred at (gu) : 89.60181 91.54065 93.27676 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 111859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17156 grid for indexing accessible points = 1.400000 m= 54940 mr = 80187 m= 17098 mr = 45217 m= 2793 mr = 13704 m= 217 mr = 1935 m= 8 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 3528 time to turn everything in is 1.370000 number of dielectric boundary points 45755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 14108 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) : 1.738111 object centre at (A) : 4.997001 0.7650003 17.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0896153E-02 -0.3169255 midg,1,midg; midg,igrid,midg -0.1225843 -0.2622812 1,midg,midg; igrid,midg,midg -0.3408636 -0.4048343 gauss-seidel spectral radius is 0.9991370 estimated iterations to convergence 269 setup time was (sec) 1.880000 now iterating at: 11:03:25 rms-change max change #iterations 7.341598 255.2372 at 10iterations 4.077400 109.5592 at 20iterations 2.252280 60.95280 at 30iterations 1.238348 28.76911 at 40iterations 0.6814070 16.74155 at 50iterations 0.3736673 10.04070 at 60iterations 0.2049885 4.670742 at 70iterations 0.1122672 2.595168 at 80iterations 6.1620563E-02 1.393272 at 90iterations 3.3697840E-02 0.8455779 at 100iterations 1.8558808E-02 0.4092712 at 110iterations 1.0121247E-02 0.2292595 at 120iterations 5.5484348E-03 0.1281950 at 130iterations 3.0429091E-03 6.6528320E-02 at 140iterations 1.6679937E-03 3.7426949E-02 at 150iterations 9.1004273E-04 2.0236969E-02 at 160iterations 5.0091749E-04 1.2065887E-02 at 170iterations 2.7425351E-04 6.5345764E-03 at 180iterations finished qdiffx linear iterations at : 11:03:50 total time elapsed so far: 27.18000 # loops : 180 mean,max change (kT/e) : 2.7425351E-04 6.5345764E-03 energy calculations done at 27.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.41000 DelPhi exited at 11:03:51 27.410u 0.739s 0:28.79 97.7% 0+0k 0+0io 0pf+0w