Wed Dec 21 14:22:12 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 21 2011 at 14:22:15 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! 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: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6235440 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): -35.02100 9.725000 ymin,ymax (A): -0.9360000 41.05000 zmin,zma (A): -1.574000 55.51900 x,y,z range (A): 44.74600 41.98600 57.09300 scale (grids/A): 0.6235440 object centre (A): -12.64800 20.05700 26.97250 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.3884 centred at (gu) : 90.60699 90.05357 90.63911 assigned negative charge : -286.8443 centred at (gu) : 90.50053 90.22208 90.65188 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5147 nv = 96 ne = 84 npr = 39763 no. pairs analyzed = 39763 no. exposed pairs = 2436 no. arc points = 16976 no. surface atoms = 832 nbur = 1112 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 275 mr = 2822 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6218157E-08 -2.2849221E-08 midg,1,midg; midg,igrid,midg -1.0137604E-08 -2.8923539E-08 1,midg,midg; igrid,midg,midg -2.2055053E-08 -1.5336306E-08 gauss-seidel spectral radius is 0.9866237 estimated iterations to convergence 71 setup time was (sec) 0.7500000 now iterating at: 14:22:16 rms-change max change #iterations 0.1154150 21.12069 at 10iterations 1.0796356E-02 1.646729 at 20iterations 9.9935010E-04 0.1705151 at 30iterations 9.2313479E-05 1.6021729E-02 at 40iterations 8.7488170E-06 1.4724731E-03 at 50iterations finished qdiffx linear iterations at : 14:22:22 total time elapsed so far: 5.990000 # loops : 50 mean,max change (kT/e) : 8.7488170E-06 1.4724731E-03 energy calculations done at 5.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.150000 DelPhi exited at 14:22:28 6.157u 0.605s 0:14.60 46.2% 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 21 2011 at 14:22:31 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! 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: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.870632 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): -35.02100 9.725000 ymin,ymax (A): -0.9360000 41.05000 zmin,zma (A): -1.574000 55.51900 x,y,z range (A): 44.74600 41.98600 57.09300 scale (grids/A): 1.870632 object centre (A): -12.64800 20.05700 26.97250 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.3884 centred at (gu) : 91.82158 90.16080 91.91766 assigned negative charge : -286.8443 centred at (gu) : 91.50158 90.66642 91.95585 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 55895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 20566 mr = 38622 m= 3077 mr = 15512 m= 153 mr = 1883 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 23634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 13722 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) : 0.6235440 object centre at (A) : -12.64800 20.05700 26.97250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2503156E-02 -7.2207384E-02 midg,1,midg; midg,igrid,midg -2.2033254E-02 -4.4449776E-02 1,midg,midg; igrid,midg,midg -2.0022357E-02 -3.3483908E-02 gauss-seidel spectral radius is 0.9985093 estimated iterations to convergence 205 setup time was (sec) 1.080000 now iterating at: 14:22:33 rms-change max change #iterations 3.440300 163.4965 at 10iterations 1.555399 59.45777 at 20iterations 0.7035204 27.60593 at 30iterations 0.3177872 11.55936 at 40iterations 0.1441740 5.322594 at 50iterations 6.4769045E-02 2.341507 at 60iterations 2.9460533E-02 1.057109 at 70iterations 1.3296677E-02 0.4795628 at 80iterations 6.0272189E-03 0.2206004 at 90iterations 2.7239588E-03 0.1007690 at 100iterations 1.2346669E-03 4.5913696E-02 at 110iterations 5.5713527E-04 2.0389557E-02 at 120iterations finished qdiffx linear iterations at : 14:22:51 total time elapsed so far: 19.08000 # loops : 120 mean,max change (kT/e) : 5.5713527E-04 2.0389557E-02 energy calculations done at 19.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.26000 DelPhi exited at 14:22:57 19.264u 0.789s 0:26.55 75.4% 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 21 2011 at 14:22:59 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! 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: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.805948 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): -35.02100 9.725000 ymin,ymax (A): -0.9360000 41.05000 zmin,zma (A): -1.574000 55.51900 x,y,z range (A): 44.74600 41.98600 57.09300 scale (grids/A): 2.805948 object centre (A): -12.64800 20.05700 26.97250 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.3884 centred at (gu) : 92.73238 90.24129 92.87643 assigned negative charge : -286.8443 centred at (gu) : 92.25251 90.99960 92.93376 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 129093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 66662 mr = 93346 m= 24096 mr = 55235 m= 5500 mr = 19630 m= 694 mr = 4089 m= 28 mr = 458 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 53300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 13951 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) : 1.870632 object centre at (A) : -12.64800 20.05700 26.97250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5948055 -1.094410 midg,1,midg; midg,igrid,midg -0.2577978 -0.5162759 1,midg,midg; igrid,midg,midg -0.2070404 -0.3633436 gauss-seidel spectral radius is 0.9992073 estimated iterations to convergence 280 setup time was (sec) 1.500000 now iterating at: 14:23:01 rms-change max change #iterations 8.112552 298.0881 at 10iterations 4.613233 119.6493 at 20iterations 2.610407 60.20873 at 30iterations 1.471614 35.34644 at 40iterations 0.8291413 18.90662 at 50iterations 0.4664450 10.26226 at 60iterations 0.2631050 5.742223 at 70iterations 0.1483441 3.614444 at 80iterations 8.3373800E-02 1.807487 at 90iterations 4.6925299E-02 1.055328 at 100iterations 2.6332013E-02 0.5644665 at 110iterations 1.4856935E-02 0.3279648 at 120iterations 8.3443876E-03 0.1743059 at 130iterations 4.6997629E-03 9.4463348E-02 at 140iterations 2.6458944E-03 5.6705475E-02 at 150iterations 1.4853213E-03 3.0775070E-02 at 160iterations 8.3344814E-04 1.8001556E-02 at 170iterations 4.6884498E-04 9.6917152E-03 at 180iterations finished qdiffx linear iterations at : 14:23:25 total time elapsed so far: 24.87000 # loops : 180 mean,max change (kT/e) : 4.6884498E-04 9.6917152E-03 energy calculations done at 24.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 25.05000 DelPhi exited at 14:23:26 25.059u 0.722s 0:26.78 96.2% 0+0k 0+0io 0pf+0w