Wed Dec 21 14:20:46 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+sph.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 = amb.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 14:20:46 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: 232 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6420777 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): -34.93700 10.54600 ymin,ymax (A): 0.4030000 41.32000 zmin,zma (A): -0.7420000 54.70300 x,y,z range (A): 45.48300 40.91700 55.44500 scale (grids/A): 0.6420777 object centre (A): -12.19550 20.86150 26.98050 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 90.21671 89.75468 90.59092 assigned negative charge : -283.2443 centred at (gu) : 90.10714 89.88314 90.58401 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 40055 no. pairs analyzed = 40055 no. exposed pairs = 2387 no. arc points = 16695 no. surface atoms = 819 nbur = 1125 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 3114 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1573 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6269 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9952862E-08 -3.6798802E-08 midg,1,midg; midg,igrid,midg -2.2876405E-08 -4.2690903E-08 1,midg,midg; igrid,midg,midg -4.1279975E-08 -2.4484503E-08 gauss-seidel spectral radius is 0.9873738 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 14:20:46 rms-change max change #iterations 0.1337065 26.80973 at 10iterations 1.3451218E-02 2.088377 at 20iterations 1.3060842E-03 0.2180691 at 30iterations 1.3348495E-04 2.0145774E-02 at 40iterations 1.3598035E-05 1.9900799E-03 at 50iterations finished qdiffx linear iterations at : 14:20:50 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.3598035E-05 1.9900799E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 14:20:50 3.598u 0.183s 0:04.38 86.0% 0+0k 0+0io 6pf+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 14:20:50 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: 232 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926233 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): -34.93700 10.54600 ymin,ymax (A): 0.4030000 41.32000 zmin,zma (A): -0.7420000 54.70300 x,y,z range (A): 45.48300 40.91700 55.44500 scale (grids/A): 1.926233 object centre (A): -12.19550 20.86150 26.98050 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 90.65052 89.26419 91.77305 assigned negative charge : -283.2443 centred at (gu) : 90.32153 89.64953 91.75235 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 22408 mr = 40859 m= 3573 mr = 17168 m= 187 mr = 2280 m= 4 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.3100000 number of dielectric boundary points 24621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 13774 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) : 0.6420777 object centre at (A) : -12.19550 20.86150 26.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6539267E-02 -6.7787059E-02 midg,1,midg; midg,igrid,midg -2.5087772E-02 -4.9772222E-02 1,midg,midg; igrid,midg,midg -2.3133993E-02 -3.7738301E-02 gauss-seidel spectral radius is 0.9985868 estimated iterations to convergence 211 setup time was (sec) 0.5900000 now iterating at: 14:20:51 rms-change max change #iterations 3.599512 146.4958 at 10iterations 1.667574 63.01477 at 20iterations 0.7725850 25.15831 at 30iterations 0.3567813 13.36243 at 40iterations 0.1650333 5.391052 at 50iterations 7.6180153E-02 2.847598 at 60iterations 3.5277694E-02 1.324343 at 70iterations 1.6245989E-02 0.6001053 at 80iterations 7.5089633E-03 0.2663498 at 90iterations 3.4697021E-03 0.1353455 at 100iterations 1.6057391E-03 5.6671143E-02 at 110iterations 7.4197806E-04 2.5182724E-02 at 120iterations finished qdiffx linear iterations at : 14:21:01 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 7.4197806E-04 2.5182724E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.92000 DelPhi exited at 14:21:02 10.924u 0.368s 0:12.02 93.8% 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 Wed Dec 21 2011 at 14:21:03 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: 232 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.889350 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): -34.93700 10.54600 ymin,ymax (A): 0.4030000 41.32000 zmin,zma (A): -0.7420000 54.70300 x,y,z range (A): 45.48300 40.91700 55.44500 scale (grids/A): 2.889350 object centre (A): -12.19550 20.86150 26.98050 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 90.97596 88.89633 92.65948 assigned negative charge : -283.2443 centred at (gu) : 90.48225 89.47441 92.62854 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 135526 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 71647 mr = 98450 m= 27267 mr = 59845 m= 6419 mr = 22671 m= 817 mr = 4822 m= 43 mr = 511 m= 0 mr = 21 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 0.8400000 number of dielectric boundary points 55399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 13952 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) : 1.926233 object centre at (A) : -12.19550 20.86150 26.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7772892 -1.059116 midg,1,midg; midg,igrid,midg -0.2365020 -0.5154951 1,midg,midg; igrid,midg,midg -0.2268370 -0.3737759 gauss-seidel spectral radius is 0.9992281 estimated iterations to convergence 284 setup time was (sec) 1.130000 now iterating at: 14:21:04 rms-change max change #iterations 8.383007 365.3388 at 10iterations 4.832475 142.5548 at 20iterations 2.754720 61.53474 at 30iterations 1.574383 38.31430 at 40iterations 0.8952039 21.45562 at 50iterations 0.5097098 10.28657 at 60iterations 0.2895674 6.258074 at 70iterations 0.1645692 3.454861 at 80iterations 9.3196370E-02 1.886475 at 90iterations 5.2956853E-02 1.108324 at 100iterations 3.0123083E-02 0.6722016 at 110iterations 1.7064931E-02 0.4067364 at 120iterations 9.6749570E-03 0.1893711 at 130iterations 5.4976097E-03 0.1073437 at 140iterations 3.1252420E-03 6.2978268E-02 at 150iterations 1.7791474E-03 4.1187286E-02 at 160iterations 1.0116876E-03 2.1184921E-02 at 170iterations 5.7859870E-04 1.2057304E-02 at 180iterations finished qdiffx linear iterations at : 14:21:20 total time elapsed so far: 16.64000 # loops : 180 mean,max change (kT/e) : 5.7859870E-04 1.2057304E-02 energy calculations done at 16.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.78000 DelPhi exited at 14:21:25 16.782u 0.372s 0:23.63 72.5% 0+0k 0+0io 0pf+0w