Sat Oct 8 16:18:25 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+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 Sat Oct 8 2011 at 16:18:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! 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 : 2336 net assigned charge : 2.000000 assigned positive charge : 357.7560 centred at (gu) : 89.13310 91.21441 90.45687 assigned negative charge : -355.7567 centred at (gu) : 89.16364 91.06476 90.54745 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 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 = 0.1200000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2700000 number of dielectric boundary points 3467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2108 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5674546E-08 -1.0796985E-08 midg,1,midg; midg,igrid,midg -1.4469480E-08 3.3526963E-08 1,midg,midg; igrid,midg,midg 1.0100380E-08 -5.3719290E-10 gauss-seidel spectral radius is 0.9878138 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 16:18:26 rms-change max change #iterations 0.1502270 19.93608 at 10iterations 1.5595647E-02 2.260872 at 20iterations 1.6912217E-03 0.2264633 at 30iterations 2.1319449E-04 2.7597427E-02 at 40iterations 4.1831412E-05 5.3048134E-03 at 50iterations finished qdiffx linear iterations at : 16:18:29 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 4.1831412E-05 5.3048134E-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) 4.140000 DelPhi exited at 16:18:30 4.145u 0.238s 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 16:18:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! 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 : 2336 net assigned charge : 2.000000 assigned positive charge : 357.7560 centred at (gu) : 87.39899 93.64280 91.37021 assigned negative charge : -355.7567 centred at (gu) : 87.49079 93.19411 91.64219 start vw surface at 0.1400000 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 = 0.2800000 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 0.5800000 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 0.7000000 number of grid points assigned charge 18433 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 3.0242365E-02 -2.2132188E-02 midg,1,midg; midg,igrid,midg -8.5130148E-03 2.7845398E-02 1,midg,midg; igrid,midg,midg -2.8189763E-02 4.1086871E-05 gauss-seidel spectral radius is 0.9986882 estimated iterations to convergence 219 setup time was (sec) 0.8900000 now iterating at: 16:18:31 rms-change max change #iterations 4.259989 205.1140 at 10iterations 2.023127 78.09514 at 20iterations 0.9643205 31.80069 at 30iterations 0.4605716 13.50724 at 40iterations 0.2180031 6.813583 at 50iterations 0.1043219 3.451115 at 60iterations 4.9467664E-02 1.507505 at 70iterations 2.3599967E-02 0.6959534 at 80iterations 1.1254282E-02 0.3822174 at 90iterations 5.3680842E-03 0.1603508 at 100iterations 2.5740704E-03 8.7108612E-02 at 110iterations 1.2323299E-03 3.8204193E-02 at 120iterations finished qdiffx linear iterations at : 16:18:39 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 1.2323299E-03 3.8204193E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 16:18:40 9.509u 0.264s 0:10.07 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 Sat Oct 8 2011 at 16:18:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! 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 : 2336 net assigned charge : 2.000000 assigned positive charge : 357.7560 centred at (gu) : 86.09835 95.46391 92.05523 assigned negative charge : -355.7567 centred at (gu) : 86.23618 94.79113 92.46310 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 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 1.500000 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 18688 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 0.2920837 -0.2567427 midg,1,midg; midg,igrid,midg -0.1107436 0.1972210 1,midg,midg; igrid,midg,midg -0.4015094 3.5136484E-02 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.840000 now iterating at: 16:18:42 rms-change max change #iterations 10.02029 421.7039 at 10iterations 5.926554 136.4153 at 20iterations 3.487267 86.61485 at 30iterations 2.050594 45.68425 at 40iterations 1.199393 23.89844 at 50iterations 0.6984249 13.05642 at 60iterations 0.4078471 7.603006 at 70iterations 0.2375355 4.232157 at 80iterations 0.1379228 2.539371 at 90iterations 7.9895675E-02 1.397121 at 100iterations 4.6313148E-02 0.8231535 at 110iterations 2.6832728E-02 0.4793677 at 120iterations 1.5531424E-02 0.2752304 at 130iterations 9.0011759E-03 0.1591830 at 140iterations 5.2002817E-03 9.4818115E-02 at 150iterations 3.0084674E-03 5.4690361E-02 at 160iterations 1.7412169E-03 3.3282280E-02 at 170iterations 1.0053472E-03 1.8207133E-02 at 180iterations finished qdiffx linear iterations at : 16:18:55 total time elapsed so far: 15.20000 # loops : 180 mean,max change (kT/e) : 1.0053472E-03 1.8207133E-02 energy calculations done at 15.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.39000 DelPhi exited at 16:18:56 15.390u 0.283s 0:15.94 98.3% 0+0k 0+0io 0pf+0w