Tue Nov 22 14:10:01 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 Tue Nov 22 2011 at 14:10:05 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 0.6120414 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): -9.045000 49.12100 ymin,ymax (A): 8.866000 47.49900 zmin,zma (A): -3.624000 38.90800 x,y,z range (A): 58.16600 38.63300 42.53200 scale (grids/A): 0.6120414 object centre (A): 20.03800 28.18250 17.64200 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 288.6021 centred at (gu) : 90.11821 89.71420 90.51553 assigned negative charge : -283.6023 centred at (gu) : 90.09550 89.62874 90.63268 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4944 nv = 96 ne = 84 npr = 40081 no. pairs analyzed = 40081 no. exposed pairs = 2487 no. arc points = 17397 no. surface atoms = 840 nbur = 1126 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 215 mr = 2682 m= 2 mr = 15 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 2464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1806 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6012 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8081052E-09 -1.5710032E-09 midg,1,midg; midg,igrid,midg -1.5100735E-10 6.0470424E-09 1,midg,midg; igrid,midg,midg 2.2549032E-09 4.1642840E-09 gauss-seidel spectral radius is 0.9861247 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 14:10:09 rms-change max change #iterations 0.1028174 20.58621 at 10iterations 9.2115039E-03 1.765400 at 20iterations 8.0587721E-04 0.1376762 at 30iterations 7.0535709E-05 1.1510253E-02 at 40iterations 6.3044390E-06 1.1081696E-03 at 50iterations finished qdiffx linear iterations at : 14:10:18 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 6.3044390E-06 1.1081696E-03 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 14:10:19 3.925u 0.223s 0:15.01 27.5% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:10:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 1.836124 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): -9.045000 49.12100 ymin,ymax (A): 8.866000 47.49900 zmin,zma (A): -3.624000 38.90800 x,y,z range (A): 58.16600 38.63300 42.53200 scale (grids/A): 1.836124 object centre (A): 20.03800 28.18250 17.64200 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 288.6021 centred at (gu) : 90.35471 89.14275 91.54649 assigned negative charge : -283.6023 centred at (gu) : 90.28668 88.88651 91.89833 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 53626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 17872 mr = 36501 m= 2208 mr = 13240 m= 78 mr = 1288 m= 0 mr = 17 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1451 time to turn everything in is 0.2700000 number of dielectric boundary points 22738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14360 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) : 0.6120414 object centre at (A) : 20.03800 28.18250 17.64200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0518419E-02 -2.3040732E-03 midg,1,midg; midg,igrid,midg 1.5804591E-03 7.7234157E-03 1,midg,midg; igrid,midg,midg 3.1361949E-02 4.1236389E-02 gauss-seidel spectral radius is 0.9984565 estimated iterations to convergence 202 setup time was (sec) 0.5200000 now iterating at: 14:10:28 rms-change max change #iterations 3.306182 142.8706 at 10iterations 1.468455 71.58189 at 20iterations 0.6560225 24.02701 at 30iterations 0.2926378 11.90800 at 40iterations 0.1312490 5.072617 at 50iterations 5.8300845E-02 2.116581 at 60iterations 2.6050990E-02 0.9323673 at 70iterations 1.1613277E-02 0.4729557 at 80iterations 5.1737055E-03 0.2070408 at 90iterations 2.3132844E-03 0.1024303 at 100iterations 1.0316982E-03 4.5364380E-02 at 110iterations 4.6007003E-04 1.7383575E-02 at 120iterations finished qdiffx linear iterations at : 14:10:54 total time elapsed so far: 8.900000 # loops : 120 mean,max change (kT/e) : 4.6007003E-04 1.7383575E-02 energy calculations done at 8.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.030000 DelPhi exited at 14:10:55 9.030u 0.276s 0:31.81 29.2% 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 Tue Nov 22 2011 at 14:10:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 2.754186 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): -9.045000 49.12100 ymin,ymax (A): 8.866000 47.49900 zmin,zma (A): -3.624000 38.90800 x,y,z range (A): 58.16600 38.63300 42.53200 scale (grids/A): 2.754186 object centre (A): 20.03800 28.18250 17.64200 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 288.6021 centred at (gu) : 90.53219 88.71406 92.31979 assigned negative charge : -283.6023 centred at (gu) : 90.43005 88.32981 92.84756 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 124430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 59471 mr = 88966 m= 19387 mr = 48704 m= 3815 mr = 15530 m= 325 mr = 2801 m= 7 mr = 206 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 5084 time to turn everything in is 0.7100000 number of dielectric boundary points 51226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14672 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) : 1.836124 object centre at (A) : 20.03800 28.18250 17.64200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9528376E-02 -3.3320622E-03 midg,1,midg; midg,igrid,midg 4.6653833E-02 6.4656235E-02 1,midg,midg; igrid,midg,midg 0.3728005 0.4950913 gauss-seidel spectral radius is 0.9991909 estimated iterations to convergence 278 setup time was (sec) 0.9900000 now iterating at: 14:11:05 rms-change max change #iterations 7.863782 317.4524 at 10iterations 4.457960 125.7862 at 20iterations 2.518169 59.99110 at 30iterations 1.410402 31.62027 at 40iterations 0.7914118 17.89546 at 50iterations 0.4426354 9.799923 at 60iterations 0.2481586 5.201866 at 70iterations 0.1386681 3.056839 at 80iterations 7.7600412E-02 1.641827 at 90iterations 4.3432262E-02 0.9658241 at 100iterations 2.4276730E-02 0.5086498 at 110iterations 1.3577954E-02 0.3118057 at 120iterations 7.5860536E-03 0.1633415 at 130iterations 4.2469883E-03 8.8192463E-02 at 140iterations 2.3768579E-03 4.7756195E-02 at 150iterations 1.3232440E-03 2.6762009E-02 at 160iterations 7.4118190E-04 1.7211914E-02 at 170iterations 4.1446596E-04 8.4304810E-03 at 180iterations finished qdiffx linear iterations at : 14:11:44 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 4.1446596E-04 8.4304810E-03 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 14:11:45 14.023u 0.270s 0:46.86 30.4% 0+0k 0+0io 0pf+0w