Sun Oct 9 02:33:44 PDT 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 Sun Oct 9 2011 at 02:33:44 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2060 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 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: 0.7509440 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): -43.11300 0.4280000 ymin,ymax (A): -19.22700 28.18000 zmin,zma (A): -38.64100 4.808000 x,y,z range (A): 43.54100 47.40700 43.44900 scale (grids/A): 0.7509440 object centre (A): -21.34250 4.476501 -16.91650 number of atom coordinates read : 2060 total number of charged atoms : 1946 net assigned charge : -4.279984 assigned positive charge : 309.4867 centred at (gu) : 88.76688 91.54779 90.97926 assigned negative charge : -313.7671 centred at (gu) : 88.79002 91.51117 90.96838 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8122 nv = 96 ne = 84 npr = 42566 no. pairs analyzed = 42566 no. exposed pairs = 2249 no. arc points = 15434 no. surface atoms = 769 nbur = 1291 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 612 mr = 5149 m= 9 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 191 time to turn everything in is 0.1700000 number of dielectric boundary points 3414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1117 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8419 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2097459E-08 -9.8440154E-08 midg,1,midg; midg,igrid,midg -1.0720132E-07 -6.6369104E-08 1,midg,midg; igrid,midg,midg -8.3873211E-08 -1.0011129E-07 gauss-seidel spectral radius is 0.9907441 estimated iterations to convergence 84 setup time was (sec) 0.3600000 now iterating at: 02:33:45 rms-change max change #iterations 0.2658800 37.07090 at 10iterations 3.7149277E-02 5.243796 at 20iterations 5.1613464E-03 0.6175537 at 30iterations 7.3211978E-04 8.5805893E-02 at 40iterations 1.0294358E-04 1.2161255E-02 at 50iterations finished qdiffx linear iterations at : 02:33:48 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.0294358E-04 1.2161255E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 02:33:48 3.458u 0.186s 0:03.94 92.1% 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 Sun Oct 9 2011 at 02:33:48 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2060 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 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: 2.252832 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): -43.11300 0.4280000 ymin,ymax (A): -19.22700 28.18000 zmin,zma (A): -38.64100 4.808000 x,y,z range (A): 43.54100 47.40700 43.44900 scale (grids/A): 2.252832 object centre (A): -21.34250 4.476501 -16.91650 number of atom coordinates read : 2060 total number of charged atoms : 1946 net assigned charge : -4.279984 assigned positive charge : 309.4867 centred at (gu) : 86.30069 94.64320 92.93745 assigned negative charge : -313.7671 centred at (gu) : 86.37016 94.53364 92.90511 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 85696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15434 grid for indexing accessible points = 1.400000 m= 37307 mr = 63828 m= 9192 mr = 30321 m= 1232 mr = 7057 m= 43 mr = 913 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4820 time to turn everything in is 0.4200000 number of dielectric boundary points 31346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15515 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) : 0.7509440 object centre at (A) : -21.34250 4.476501 -16.91650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6042738E-03 -3.8636480E-02 midg,1,midg; midg,igrid,midg 1.3018195E-02 -5.9268419E-02 1,midg,midg; igrid,midg,midg -3.4584820E-02 -2.1184443E-02 gauss-seidel spectral radius is 0.9989327 estimated iterations to convergence 242 setup time was (sec) 0.6600000 now iterating at: 02:33:49 rms-change max change #iterations 5.166574 229.2537 at 10iterations 2.647908 82.34706 at 20iterations 1.354048 38.29422 at 30iterations 0.6965516 21.80555 at 40iterations 0.3564107 10.08190 at 50iterations 0.1818984 5.292717 at 60iterations 9.3554229E-02 2.685381 at 70iterations 4.8038822E-02 1.377172 at 80iterations 2.4545126E-02 0.6551998 at 90iterations 1.2629052E-02 0.3674088 at 100iterations 6.4782090E-03 0.1774521 at 110iterations 3.3145272E-03 9.3261719E-02 at 120iterations finished qdiffx linear iterations at : 02:33:57 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 3.3145272E-03 9.3261719E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 02:33:57 8.265u 0.223s 0:08.75 96.9% 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 Sun Oct 9 2011 at 02:33:57 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2060 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 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: 3.379248 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): -43.11300 0.4280000 ymin,ymax (A): -19.22700 28.18000 zmin,zma (A): -38.64100 4.808000 x,y,z range (A): 43.54100 47.40700 43.44900 scale (grids/A): 3.379248 object centre (A): -21.34250 4.476501 -16.91650 number of atom coordinates read : 2060 total number of charged atoms : 1946 net assigned charge : -4.279984 assigned positive charge : 309.4867 centred at (gu) : 84.45090 96.96470 94.40622 assigned negative charge : -313.7671 centred at (gu) : 84.55534 96.80047 94.35780 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 197484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15434 grid for indexing accessible points = 1.400000 m= 112714 mr = 152454 m= 51750 mr = 97379 m= 18260 mr = 45182 m= 4855 mr = 15551 m= 854 mr = 4132 m= 46 mr = 682 m= 0 mr = 21 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 16548 time to turn everything in is 1.370000 number of dielectric boundary points 70562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 15568 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) : 2.252832 object centre at (A) : -21.34250 4.476501 -16.91650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1523188 -0.2724618 midg,1,midg; midg,igrid,midg 0.2992342 -0.7115613 1,midg,midg; igrid,midg,midg -0.3724905 -0.1307742 gauss-seidel spectral radius is 0.9993096 estimated iterations to convergence 300 setup time was (sec) 1.620000 now iterating at: 02:33:59 rms-change max change #iterations 10.98812 295.8989 at 10iterations 6.466495 130.8199 at 20iterations 3.809700 69.26622 at 30iterations 2.234262 36.72710 at 40iterations 1.313958 19.76185 at 50iterations 0.7698263 12.47312 at 60iterations 0.4523610 7.132102 at 70iterations 0.2650993 4.220448 at 80iterations 0.1553883 2.562060 at 90iterations 9.1270946E-02 1.494900 at 100iterations 5.3512625E-02 0.8017163 at 110iterations 3.1437721E-02 0.5002441 at 120iterations 1.8414563E-02 0.2861139 at 130iterations 1.0826251E-02 0.1702445 at 140iterations 6.3606822E-03 9.5222473E-02 at 150iterations 3.7424935E-03 6.0404778E-02 at 160iterations 2.2102615E-03 4.3251470E-02 at 170iterations 1.3104930E-03 2.1968842E-02 at 180iterations finished qdiffx linear iterations at : 02:34:11 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 1.3104930E-03 2.1968842E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 02:34:12 13.830u 0.245s 0:14.36 97.9% 0+0k 0+0io 0pf+0w