Sat Oct 8 16:18:56 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 Sat Oct 8 2011 at 16:18:56 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 !!! WARNING: GLU 258 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6525286 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): -46.19800 2.125000 ymin,ymax (A): 4.067000 49.54000 zmin,zma (A): -17.93600 36.62100 x,y,z range (A): 48.32300 45.47300 54.55700 scale (grids/A): 0.6525286 object centre (A): -22.03650 26.80350 9.342500 number of atom coordinates read : 2402 total number of charged atoms : 2332 net assigned charge : 1.806002 assigned positive charge : 359.2960 centred at (gu) : 89.10607 91.23105 90.43698 assigned negative charge : -357.4907 centred at (gu) : 89.13567 91.07726 90.53113 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6962 nv = 96 ne = 84 npr = 48094 no. pairs analyzed = 48094 no. exposed pairs = 3076 no. arc points = 20851 no. surface atoms = 1055 nbur = 1347 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3853 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2800000 number of dielectric boundary points 3467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5897514E-08 -1.1874220E-08 midg,1,midg; midg,igrid,midg -1.5318232E-08 3.4036418E-08 1,midg,midg; igrid,midg,midg 9.5179002E-09 -7.8009421E-10 gauss-seidel spectral radius is 0.9878138 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 16:18:57 rms-change max change #iterations 0.1526038 19.92133 at 10iterations 1.5819078E-02 2.203007 at 20iterations 1.7021514E-03 0.2272902 at 30iterations 2.0474213E-04 2.7909279E-02 at 40iterations 3.7531052E-05 4.8465729E-03 at 50iterations finished qdiffx linear iterations at : 16:19:00 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.7531052E-05 4.8465729E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 16:19:01 4.137u 0.245s 0:04.65 93.9% 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 Sat Oct 8 2011 at 16:19:01 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 !!! WARNING: GLU 258 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.957586 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): -46.19800 2.125000 ymin,ymax (A): 4.067000 49.54000 zmin,zma (A): -17.93600 36.62100 x,y,z range (A): 48.32300 45.47300 54.55700 scale (grids/A): 1.957586 object centre (A): -22.03650 26.80350 9.342500 number of atom coordinates read : 2402 total number of charged atoms : 2332 net assigned charge : 1.806002 assigned positive charge : 359.2960 centred at (gu) : 87.31786 93.69270 91.31052 assigned negative charge : -357.4907 centred at (gu) : 87.40689 93.23159 91.59326 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20851 grid for indexing accessible points = 1.400000 m= 28271 mr = 52214 m= 4905 mr = 21131 m= 287 mr = 3129 m= 9 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 0.5700000 number of dielectric boundary points 31789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18403 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) : 0.6525286 object centre at (A) : -22.03650 26.80350 9.342500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0934630E-02 -2.2351624E-02 midg,1,midg; midg,igrid,midg -9.6743479E-03 2.7664805E-02 1,midg,midg; igrid,midg,midg -2.9313715E-02 -2.7118390E-04 gauss-seidel spectral radius is 0.9986882 estimated iterations to convergence 219 setup time was (sec) 0.9100000 now iterating at: 16:19:02 rms-change max change #iterations 4.291499 205.1140 at 10iterations 2.038023 78.09515 at 20iterations 0.9712619 30.55125 at 30iterations 0.4639839 13.60295 at 40iterations 0.2195311 6.748278 at 50iterations 0.1050455 3.435792 at 60iterations 4.9816824E-02 1.574198 at 70iterations 2.3764513E-02 0.6832237 at 80iterations 1.1329275E-02 0.3933868 at 90iterations 5.4022376E-03 0.1587830 at 100iterations 2.5869783E-03 8.5033417E-02 at 110iterations 1.2377793E-03 3.7514687E-02 at 120iterations finished qdiffx linear iterations at : 16:19:10 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 1.2377793E-03 3.7514687E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 16:19:11 9.584u 0.263s 0:10.16 96.8% 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 Sat Oct 8 2011 at 16:19:11 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 !!! WARNING: GLU 258 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.936378 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): -46.19800 2.125000 ymin,ymax (A): 4.067000 49.54000 zmin,zma (A): -17.93600 36.62100 x,y,z range (A): 48.32300 45.47300 54.55700 scale (grids/A): 2.936378 object centre (A): -22.03650 26.80350 9.342500 number of atom coordinates read : 2402 total number of charged atoms : 2332 net assigned charge : 1.806002 assigned positive charge : 359.2960 centred at (gu) : 85.97666 95.53876 91.96570 assigned negative charge : -357.4907 centred at (gu) : 86.11034 94.84738 92.38971 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 173082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20851 grid for indexing accessible points = 1.400000 m= 89415 mr = 126397 m= 34789 mr = 73625 m= 9032 mr = 28333 m= 1342 mr = 6901 m= 89 mr = 825 m= 5 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 2595 time to turn everything in is 1.490000 number of dielectric boundary points 71643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 18656 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) : 1.957586 object centre at (A) : -22.03650 26.80350 9.342500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2980422 -0.2580909 midg,1,midg; midg,igrid,midg -0.1232752 0.1950310 1,midg,midg; igrid,midg,midg -0.4209355 3.2307051E-02 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.830000 now iterating at: 16:19:13 rms-change max change #iterations 10.08762 421.7037 at 10iterations 5.964941 136.4142 at 20iterations 3.509458 86.53482 at 30iterations 2.063368 44.68130 at 40iterations 1.206579 23.87831 at 50iterations 0.7023391 13.85583 at 60iterations 0.4100463 7.545148 at 70iterations 0.2388271 4.236553 at 80iterations 0.1386283 2.547516 at 90iterations 8.0309793E-02 1.373688 at 100iterations 4.6557870E-02 0.8299494 at 110iterations 2.6974605E-02 0.4751863 at 120iterations 1.5609550E-02 0.2844124 at 130iterations 9.0482393E-03 0.1611190 at 140iterations 5.2280361E-03 9.3913078E-02 at 150iterations 3.0249518E-03 5.6038857E-02 at 160iterations 1.7509516E-03 3.3264160E-02 at 170iterations 1.0118580E-03 1.8197060E-02 at 180iterations finished qdiffx linear iterations at : 16:19:26 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 1.0118580E-03 1.8197060E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 16:19:27 15.422u 0.285s 0:15.97 98.3% 0+0k 0+0io 0pf+0w