Wed Dec 21 14:21:21 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 14:21:25 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: 271 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: 0.6234567 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): -35.14900 10.12600 ymin,ymax (A): 1.130000 41.35300 zmin,zma (A): -0.6190000 56.48200 x,y,z range (A): 45.27500 40.22300 57.10100 scale (grids/A): 0.6234567 object centre (A): -12.51150 21.24150 27.93150 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.7884 centred at (gu) : 90.40347 89.51972 89.96002 assigned negative charge : -287.2443 centred at (gu) : 90.30756 89.67863 89.99421 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5198 nv = 96 ne = 84 npr = 39548 no. pairs analyzed = 39548 no. exposed pairs = 2500 no. arc points = 17559 no. surface atoms = 853 nbur = 1091 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2779 m= 0 mr = 41 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 2673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7542948E-08 -2.0936019E-08 midg,1,midg; midg,igrid,midg -1.1858968E-08 -2.5296712E-08 1,midg,midg; igrid,midg,midg -2.2495305E-08 -1.5319479E-08 gauss-seidel spectral radius is 0.9866214 estimated iterations to convergence 71 setup time was (sec) 0.3600000 now iterating at: 14:21:26 rms-change max change #iterations 0.1207415 21.16278 at 10iterations 1.1252810E-02 1.801134 at 20iterations 1.0433893E-03 0.1878724 at 30iterations 9.5961528E-05 1.6471863E-02 at 40iterations 9.0423737E-06 1.4953613E-03 at 50iterations finished qdiffx linear iterations at : 14:21:30 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 9.0423737E-06 1.4953613E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 14:21:32 3.710u 0.262s 0:08.03 49.4% 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 14:21:38 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: 271 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: 1.870370 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): -35.14900 10.12600 ymin,ymax (A): 1.130000 41.35300 zmin,zma (A): -0.6190000 56.48200 x,y,z range (A): 45.27500 40.22300 57.10100 scale (grids/A): 1.870370 object centre (A): -12.51150 21.24150 27.93150 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.7884 centred at (gu) : 91.21087 88.55943 89.88018 assigned negative charge : -287.2443 centred at (gu) : 90.92290 89.03606 89.98284 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 55983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17559 grid for indexing accessible points = 1.400000 m= 20677 mr = 38182 m= 3232 mr = 15291 m= 221 mr = 2049 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 330 time to turn everything in is 0.3000000 number of dielectric boundary points 24520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 13715 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) : 0.6234567 object centre at (A) : -12.51150 21.24150 27.93150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1304527E-02 -6.3490964E-02 midg,1,midg; midg,igrid,midg -2.1638870E-02 -3.7732344E-02 1,midg,midg; igrid,midg,midg -2.4300603E-02 -3.3127762E-02 gauss-seidel spectral radius is 0.9985120 estimated iterations to convergence 206 setup time was (sec) 0.5100000 now iterating at: 14:21:43 rms-change max change #iterations 3.490613 165.1119 at 10iterations 1.588919 66.62150 at 20iterations 0.7148820 26.63371 at 30iterations 0.3236451 11.74401 at 40iterations 0.1464559 5.243984 at 50iterations 6.6276908E-02 2.490768 at 60iterations 2.9969992E-02 1.135089 at 70iterations 1.3604165E-02 0.4753647 at 80iterations 6.1684684E-03 0.2341785 at 90iterations 2.7782349E-03 0.1057339 at 100iterations 1.2553731E-03 4.5970917E-02 at 110iterations 5.7101058E-04 2.0410538E-02 at 120iterations finished qdiffx linear iterations at : 14:21:52 total time elapsed so far: 8.890000 # loops : 120 mean,max change (kT/e) : 5.7101058E-04 2.0410538E-02 energy calculations done at 8.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 14:22:04 9.023u 0.260s 0:26.85 34.5% 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 14:22:13 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: 271 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: 2.805555 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): -35.14900 10.12600 ymin,ymax (A): 1.130000 41.35300 zmin,zma (A): -0.6190000 56.48200 x,y,z range (A): 45.27500 40.22300 57.10100 scale (grids/A): 2.805555 object centre (A): -12.51150 21.24150 27.93150 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 265.7884 centred at (gu) : 91.81633 87.83921 89.82038 assigned negative charge : -287.2443 centred at (gu) : 91.38441 88.55415 89.97425 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 129257 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17559 grid for indexing accessible points = 1.400000 m= 66495 mr = 92438 m= 24340 mr = 54425 m= 5621 mr = 19692 m= 791 mr = 4220 m= 46 mr = 499 m= 0 mr = 11 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1133 time to turn everything in is 0.7400000 number of dielectric boundary points 55265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8300000 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) : 1.870370 object centre at (A) : -12.51150 21.24150 27.93150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7562387 -0.9466053 midg,1,midg; midg,igrid,midg -0.2427761 -0.4228019 1,midg,midg; igrid,midg,midg -0.2506233 -0.3512612 gauss-seidel spectral radius is 0.9992093 estimated iterations to convergence 281 setup time was (sec) 0.9700000 now iterating at: 14:22:17 rms-change max change #iterations 8.246148 299.6790 at 10iterations 4.715909 120.5272 at 20iterations 2.667694 64.60159 at 30iterations 1.511801 34.31500 at 40iterations 0.8540456 19.71038 at 50iterations 0.4816776 10.29270 at 60iterations 0.2707994 5.877419 at 70iterations 0.1533479 3.159107 at 80iterations 8.6232692E-02 2.090611 at 90iterations 4.8651811E-02 1.071095 at 100iterations 2.7410766E-02 0.5425720 at 110iterations 1.5398067E-02 0.3199043 at 120iterations 8.6768353E-03 0.1875229 at 130iterations 4.8839059E-03 0.1073966 at 140iterations 2.7525420E-03 6.0115814E-02 at 150iterations 1.5496054E-03 3.3294678E-02 at 160iterations 8.7282457E-04 1.8349648E-02 at 170iterations 4.9136241E-04 1.0326385E-02 at 180iterations finished qdiffx linear iterations at : 14:22:30 total time elapsed so far: 14.25000 # loops : 180 mean,max change (kT/e) : 4.9136241E-04 1.0326385E-02 energy calculations done at 14.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.39000 DelPhi exited at 14:22:40 14.390u 0.239s 0:28.04 52.1% 0+0k 0+0io 0pf+0w