Wed Dec 28 11:02:26 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 11:02:26 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! 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: 0.6245394 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): -35.16800 9.842000 ymin,ymax (A): 1.252000 41.42500 zmin,zma (A): -0.2290000 56.77300 x,y,z range (A): 45.01000 40.17300 57.00200 scale (grids/A): 0.6245394 object centre (A): -12.66300 21.33850 28.27200 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 268.2703 centred at (gu) : 90.49483 89.45896 89.74801 assigned negative charge : -290.2222 centred at (gu) : 90.39684 89.62471 89.76997 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5237 nv = 96 ne = 84 npr = 39796 no. pairs analyzed = 39796 no. exposed pairs = 2488 no. arc points = 17272 no. surface atoms = 846 nbur = 1114 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 262 mr = 2884 m= 0 mr = 29 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1630 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6049 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0160169E-08 -2.0482918E-08 midg,1,midg; midg,igrid,midg -1.2424151E-08 -2.6648429E-08 1,midg,midg; igrid,midg,midg -2.3371163E-08 -1.6473180E-08 gauss-seidel spectral radius is 0.9866678 estimated iterations to convergence 71 setup time was (sec) 0.7800000 now iterating at: 11:02:27 rms-change max change #iterations 0.1209343 20.85578 at 10iterations 1.1473151E-02 1.834955 at 20iterations 1.0418709E-03 0.1785002 at 30iterations 9.7170843E-05 1.6258240E-02 at 40iterations 9.3526251E-06 1.5697479E-03 at 50iterations finished qdiffx linear iterations at : 11:02:32 total time elapsed so far: 5.500000 # loops : 50 mean,max change (kT/e) : 9.3526251E-06 1.5697479E-03 energy calculations done at 5.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.730000 DelPhi exited at 11:02:34 5.734u 0.651s 0:07.97 80.0% 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 11:02:34 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.873618 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): -35.16800 9.842000 ymin,ymax (A): 1.252000 41.42500 zmin,zma (A): -0.2290000 56.77300 x,y,z range (A): 45.01000 40.17300 57.00200 scale (grids/A): 1.873618 object centre (A): -12.66300 21.33850 28.27200 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 268.2703 centred at (gu) : 91.48475 88.37713 89.24402 assigned negative charge : -290.2222 centred at (gu) : 91.19076 88.87424 89.30994 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17272 grid for indexing accessible points = 1.400000 m= 20957 mr = 38922 m= 3149 mr = 15793 m= 159 mr = 2081 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 23850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 13868 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) : 0.6245394 object centre at (A) : -12.66300 21.33850 28.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8834940E-02 -5.9526023E-02 midg,1,midg; midg,igrid,midg -2.2653274E-02 -4.0502802E-02 1,midg,midg; igrid,midg,midg -2.3753921E-02 -3.3875398E-02 gauss-seidel spectral radius is 0.9985168 estimated iterations to convergence 206 setup time was (sec) 1.110000 now iterating at: 11:02:36 rms-change max change #iterations 3.517492 169.4189 at 10iterations 1.588418 64.71280 at 20iterations 0.7220719 26.44226 at 30iterations 0.3264482 12.03324 at 40iterations 0.1482430 5.478740 at 50iterations 6.7230754E-02 2.755249 at 60iterations 3.0519778E-02 1.123810 at 70iterations 1.3746156E-02 0.5168676 at 80iterations 6.2445416E-03 0.2291794 at 90iterations 2.8410857E-03 0.1028872 at 100iterations 1.2861082E-03 4.9774170E-02 at 110iterations 5.8296666E-04 2.1298647E-02 at 120iterations finished qdiffx linear iterations at : 11:02:51 total time elapsed so far: 16.41000 # loops : 120 mean,max change (kT/e) : 5.8296666E-04 2.1298647E-02 energy calculations done at 16.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.65000 DelPhi exited at 11:02:52 16.652u 0.754s 0:17.92 97.0% 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 11:02:52 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! 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: 2.810428 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): -35.16800 9.842000 ymin,ymax (A): 1.252000 41.42500 zmin,zma (A): -0.2290000 56.77300 x,y,z range (A): 45.01000 40.17300 57.00200 scale (grids/A): 2.810428 object centre (A): -12.66300 21.33850 28.27200 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 268.2703 centred at (gu) : 92.22723 87.56569 88.86604 assigned negative charge : -290.2222 centred at (gu) : 91.78617 88.31145 88.96494 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 130215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17272 grid for indexing accessible points = 1.400000 m= 67020 mr = 93715 m= 24849 mr = 55633 m= 5688 mr = 20416 m= 745 mr = 4395 m= 42 mr = 532 m= 0 mr = 23 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 53845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 14080 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) : 1.873618 object centre at (A) : -12.66300 21.33850 28.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9371536 -0.8178383 midg,1,midg; midg,igrid,midg -0.2548352 -0.4334189 1,midg,midg; igrid,midg,midg -0.2547744 -0.3638718 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 2.160000 now iterating at: 11:02:55 rms-change max change #iterations 8.275768 378.9563 at 10iterations 4.732708 129.4870 at 20iterations 2.687381 59.57177 at 30iterations 1.517386 33.47827 at 40iterations 0.8558369 18.90235 at 50iterations 0.4831004 9.600540 at 60iterations 0.2726584 5.981733 at 70iterations 0.1533611 3.215225 at 80iterations 8.6288549E-02 1.737724 at 90iterations 4.8509888E-02 0.9669189 at 100iterations 2.7342120E-02 0.5938891 at 110iterations 1.5406398E-02 0.3302517 at 120iterations 8.6802952E-03 0.1873426 at 130iterations 4.8776069E-03 0.1050477 at 140iterations 2.7483115E-03 5.2920938E-02 at 150iterations 1.5474074E-03 3.0923843E-02 at 160iterations 8.6909073E-04 1.8034458E-02 at 170iterations 4.8899942E-04 9.9706650E-03 at 180iterations finished qdiffx linear iterations at : 11:03:20 total time elapsed so far: 27.36000 # loops : 180 mean,max change (kT/e) : 4.8899942E-04 9.9706650E-03 energy calculations done at 27.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.60000 DelPhi exited at 11:03:21 27.604u 0.850s 0:29.09 97.7% 0+0k 0+0io 0pf+0w