Thu Jan 19 13:33:01 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:02 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6583 !!! WARNING: THR 31 has a net charge of 0.2330 !!! WARNING: SER 34 has a net charge of 0.2400 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: SER 54 has a net charge of 0.2400 !!! WARNING: ILE 58 has a net charge of -0.0170 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LEU 68 has a net charge of -0.0260 !!! WARNING: ASP 70 has a net charge of -0.2080 !!! WARNING: VAL 72 has a net charge of -0.0120 !!! WARNING: ILE 77 has a net charge of -0.0170 !!! WARNING: ILE 101 has a net charge of -0.0170 !!! WARNING: SER 115 has a net charge of 0.2400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: THR 130 has a net charge of 0.2330 !!! WARNING: THR 134 has a net charge of 0.2330 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ILE 157 has a net charge of -0.0170 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: GLN 212 has a net charge of 0.0170 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: VAL 235 has a net charge of -0.0120 !!! WARNING: VAL 240 has a net charge of -0.0120 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: ILE 248 has a net charge of -0.0170 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: VAL 256 has a net charge of -0.0120 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: SER 381 has a net charge of 0.2400 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ILE 467 has a net charge of -0.0170 !!! WARNING: SER 485 has a net charge of 0.2400 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: THR 584 has a net charge of 0.2330 !!! WARNING: SER 587 has a net charge of 0.2400 !!! WARNING: ILE 654 has a net charge of -0.0170 !!! WARNING: SER 668 has a net charge of 0.2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4407686 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): 211.7520 275.7740 ymin,ymax (A): 63.13800 140.1320 zmin,zma (A): -66.91000 13.85800 x,y,z range (A): 64.02199 76.99399 80.76801 scale (grids/A): 0.4407686 object centre (A): 243.7630 101.6350 -26.52600 number of atom coordinates read : 6583 total number of charged atoms : 6356 net assigned charge : -2.399938 assigned positive charge : 985.7481 centred at (gu) : 90.91010 89.81890 88.06142 assigned negative charge : -988.1575 centred at (gu) : 90.94431 89.79647 87.99879 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7678 nv = 96 ne = 84 npr = 130902 no. pairs analyzed = 130902 no. exposed pairs = 8939 no. arc points = 60180 no. surface atoms = 3007 nbur = 3576 mkacc time = 0.2300000 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 = 1.904000 m= 235 mr = 3497 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4997 ## 914 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4246135E-11 3.4574962E-12 midg,1,midg; midg,igrid,midg -3.4406158E-12 1.6838756E-12 1,midg,midg; igrid,midg,midg 2.3371196E-12 -6.0636778E-12 gauss-seidel spectral radius is 0.9738645 estimated iterations to convergence 52 setup time was (sec) 0.6200000 now iterating at: 13:33:02 rms-change max change #iterations 3.4088664E-02 4.894140 at 10iterations 1.8279140E-03 0.3332787 at 20iterations 5.4339430E-04 8.4606647E-02 at 30iterations 2.1799536E-04 3.7627697E-02 at 40iterations 8.7822307E-05 1.5717983E-02 at 50iterations finished qdiffx linear iterations at : 13:33:08 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 8.7822307E-05 1.5717983E-02 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 13:33:09 3.925u 0.209s 0:07.49 55.0% 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 Thu Jan 19 2012 at 13:33:09 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6583 !!! WARNING: THR 31 has a net charge of 0.2330 !!! WARNING: SER 34 has a net charge of 0.2400 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: SER 54 has a net charge of 0.2400 !!! WARNING: ILE 58 has a net charge of -0.0170 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LEU 68 has a net charge of -0.0260 !!! WARNING: ASP 70 has a net charge of -0.2080 !!! WARNING: VAL 72 has a net charge of -0.0120 !!! WARNING: ILE 77 has a net charge of -0.0170 !!! WARNING: ILE 101 has a net charge of -0.0170 !!! WARNING: SER 115 has a net charge of 0.2400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: THR 130 has a net charge of 0.2330 !!! WARNING: THR 134 has a net charge of 0.2330 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ILE 157 has a net charge of -0.0170 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: GLN 212 has a net charge of 0.0170 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: VAL 235 has a net charge of -0.0120 !!! WARNING: VAL 240 has a net charge of -0.0120 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: ILE 248 has a net charge of -0.0170 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: VAL 256 has a net charge of -0.0120 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: SER 381 has a net charge of 0.2400 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ILE 467 has a net charge of -0.0170 !!! WARNING: SER 485 has a net charge of 0.2400 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: THR 584 has a net charge of 0.2330 !!! WARNING: SER 587 has a net charge of 0.2400 !!! WARNING: ILE 654 has a net charge of -0.0170 !!! WARNING: SER 668 has a net charge of 0.2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.322306 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): 211.7520 275.7740 ymin,ymax (A): 63.13800 140.1320 zmin,zma (A): -66.91000 13.85800 x,y,z range (A): 64.02199 76.99399 80.76801 scale (grids/A): 1.322306 object centre (A): 243.7630 101.6350 -26.52600 number of atom coordinates read : 6583 total number of charged atoms : 6356 net assigned charge : -2.399938 assigned positive charge : 985.7481 centred at (gu) : 92.72842 89.45441 84.18243 assigned negative charge : -988.1575 centred at (gu) : 92.83262 89.38921 83.99609 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 88057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60180 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 22636 mr = 56702 m= 1332 mr = 13582 m= 15 mr = 341 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 256 time to turn everything in is 0.4900000 number of dielectric boundary points 41415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 926 ## 33 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 44733 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) : 0.4407686 object centre at (A) : 243.7630 101.6350 -26.52600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2188480E-03 6.0429187E-03 midg,1,midg; midg,igrid,midg 2.8029508E-03 -4.1587953E-04 1,midg,midg; igrid,midg,midg 3.0602069E-04 -2.7616841E-03 gauss-seidel spectral radius is 0.9975436 estimated iterations to convergence 161 setup time was (sec) 0.7300000 now iterating at: 13:33:10 rms-change max change #iterations 3.187228 138.0663 at 10iterations 1.149467 40.33649 at 20iterations 0.4174004 13.40379 at 30iterations 0.1507480 5.614357 at 40iterations 5.4836590E-02 1.912724 at 50iterations 1.9905321E-02 0.7395414 at 60iterations 7.3222863E-03 0.3017731 at 70iterations 2.7687885E-03 0.1185961 at 80iterations 1.1384408E-03 4.5711517E-02 at 90iterations 5.6512281E-04 2.1696091E-02 at 100iterations 3.3911457E-04 1.4258385E-02 at 110iterations 2.2716272E-04 8.8491440E-03 at 120iterations finished qdiffx linear iterations at : 13:33:25 total time elapsed so far: 8.360000 # loops : 120 mean,max change (kT/e) : 2.2716272E-04 8.8491440E-03 energy calculations done at 8.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 13:33:25 8.516u 0.227s 0:16.19 53.9% 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 Thu Jan 19 2012 at 13:33:25 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6583 !!! WARNING: THR 31 has a net charge of 0.2330 !!! WARNING: SER 34 has a net charge of 0.2400 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: SER 54 has a net charge of 0.2400 !!! WARNING: ILE 58 has a net charge of -0.0170 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LEU 68 has a net charge of -0.0260 !!! WARNING: ASP 70 has a net charge of -0.2080 !!! WARNING: VAL 72 has a net charge of -0.0120 !!! WARNING: ILE 77 has a net charge of -0.0170 !!! WARNING: ILE 101 has a net charge of -0.0170 !!! WARNING: SER 115 has a net charge of 0.2400 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: THR 130 has a net charge of 0.2330 !!! WARNING: THR 134 has a net charge of 0.2330 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ILE 157 has a net charge of -0.0170 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: GLN 212 has a net charge of 0.0170 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: VAL 235 has a net charge of -0.0120 !!! WARNING: VAL 240 has a net charge of -0.0120 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: ILE 248 has a net charge of -0.0170 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: VAL 256 has a net charge of -0.0120 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: SER 381 has a net charge of 0.2400 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ILE 467 has a net charge of -0.0170 !!! WARNING: SER 485 has a net charge of 0.2400 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: THR 584 has a net charge of 0.2330 !!! WARNING: SER 587 has a net charge of 0.2400 !!! WARNING: ILE 654 has a net charge of -0.0170 !!! WARNING: SER 668 has a net charge of 0.2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.983459 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): 211.7520 275.7740 ymin,ymax (A): 63.13800 140.1320 zmin,zma (A): -66.91000 13.85800 x,y,z range (A): 64.02199 76.99399 80.76801 scale (grids/A): 1.983459 object centre (A): 243.7630 101.6350 -26.52600 number of atom coordinates read : 6583 total number of charged atoms : 6356 net assigned charge : -2.399938 assigned positive charge : 985.7481 centred at (gu) : 94.09188 89.18130 81.27290 assigned negative charge : -988.1575 centred at (gu) : 94.24876 89.08380 80.99408 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 205867 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60180 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 83990 mr = 141553 m= 17539 mr = 61753 m= 1500 mr = 11464 m= 35 mr = 659 m= 0 mr = 2 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 1.100000 number of dielectric boundary points 93500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 50275 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) : 1.322306 object centre at (A) : 243.7630 101.6350 -26.52600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4716088 0.1740240 midg,1,midg; midg,igrid,midg 7.7958651E-02 -7.0760744E-03 1,midg,midg; igrid,midg,midg -4.9120001E-03 -4.0535975E-02 gauss-seidel spectral radius is 0.9990222 estimated iterations to convergence 253 setup time was (sec) 1.350000 now iterating at: 13:33:27 rms-change max change #iterations 9.663877 340.0627 at 10iterations 5.325353 143.0235 at 20iterations 2.905704 72.64473 at 30iterations 1.574289 38.43336 at 40iterations 0.8481110 18.12694 at 50iterations 0.4568535 9.564960 at 60iterations 0.2443917 5.768650 at 70iterations 0.1306305 3.112952 at 80iterations 6.9798551E-02 1.535812 at 90iterations 3.7035450E-02 0.8885765 at 100iterations 1.9730434E-02 0.4080191 at 110iterations 1.0482729E-02 0.2102509 at 120iterations 5.5827517E-03 0.1395540 at 130iterations 2.9720059E-03 6.7108154E-02 at 140iterations 1.5963641E-03 3.4473419E-02 at 150iterations 8.6276449E-04 1.8825531E-02 at 160iterations 4.7788836E-04 1.0547638E-02 at 170iterations 2.7460692E-04 5.9012175E-03 at 180iterations finished qdiffx linear iterations at : 13:33:40 total time elapsed so far: 14.48000 # loops : 180 mean,max change (kT/e) : 2.7460692E-04 5.9012175E-03 energy calculations done at 14.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.61000 DelPhi exited at 13:33:41 14.612u 0.237s 0:15.49 95.8% 0+0k 0+0io 0pf+0w