Sat Oct 15 13:38:18 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 15 2011 at 13:38:18 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3335 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLU 207 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: 0.5968048 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): -12.93900 45.12000 ymin,ymax (A): -9.030000 50.62100 zmin,zma (A): -14.07100 39.87600 x,y,z range (A): 58.05900 59.65100 53.94700 scale (grids/A): 0.5968048 object centre (A): 16.09050 20.79550 12.90250 number of atom coordinates read : 3335 total number of charged atoms : 3190 net assigned charge : -6.599979 assigned positive charge : 510.4935 centred at (gu) : 90.12309 90.24882 89.83038 assigned negative charge : -517.0945 centred at (gu) : 90.14926 90.37999 89.92380 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7963 nv = 96 ne = 84 npr = 66019 no. pairs analyzed = 66019 no. exposed pairs = 4601 no. arc points = 32390 no. surface atoms = 1521 nbur = 1814 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3991 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.2400000 number of dielectric boundary points 4307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3195 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6050774E-09 -6.4375114E-09 midg,1,midg; midg,igrid,midg 2.9740146E-09 -8.8911634E-09 1,midg,midg; igrid,midg,midg -1.3471888E-09 -3.7916115E-09 gauss-seidel spectral radius is 0.9855414 estimated iterations to convergence 68 setup time was (sec) 0.4600000 now iterating at: 13:38:19 rms-change max change #iterations 0.1188370 22.33036 at 10iterations 1.0028475E-02 1.440788 at 20iterations 9.2457840E-04 0.1176682 at 30iterations 1.6597201E-04 2.0889282E-02 at 40iterations 5.5016029E-05 6.0386658E-03 at 50iterations finished qdiffx linear iterations at : 13:38:23 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 5.5016029E-05 6.0386658E-03 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 13:38:24 3.820u 0.225s 0:05.88 68.7% 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 15 2011 at 13:38:24 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3335 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLU 207 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.790414 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): -12.93900 45.12000 ymin,ymax (A): -9.030000 50.62100 zmin,zma (A): -14.07100 39.87600 x,y,z range (A): 58.05900 59.65100 53.94700 scale (grids/A): 1.790414 object centre (A): 16.09050 20.79550 12.90250 number of atom coordinates read : 3335 total number of charged atoms : 3190 net assigned charge : -6.599979 assigned positive charge : 510.4935 centred at (gu) : 90.36823 90.74580 89.49017 assigned negative charge : -517.0945 centred at (gu) : 90.44725 91.13924 89.77090 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 86031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32390 grid for indexing accessible points = 1.400000 m= 28578 mr = 57170 m= 3827 mr = 19410 m= 176 mr = 2085 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3560 time to turn everything in is 0.4400000 number of dielectric boundary points 39918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 24851 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) : 0.5968048 object centre at (A) : 16.09050 20.79550 12.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9421995E-03 -1.2408080E-02 midg,1,midg; midg,igrid,midg 8.8503063E-03 -3.5632815E-02 1,midg,midg; igrid,midg,midg 1.1493209E-02 -2.6033510E-02 gauss-seidel spectral radius is 0.9985548 estimated iterations to convergence 209 setup time was (sec) 0.7100000 now iterating at: 13:38:26 rms-change max change #iterations 4.448520 180.9790 at 10iterations 2.023003 66.72138 at 20iterations 0.9246117 32.12193 at 30iterations 0.4230556 13.31280 at 40iterations 0.1938844 6.248386 at 50iterations 8.8694632E-02 3.407162 at 60iterations 4.0672079E-02 1.291458 at 70iterations 1.8615443E-02 0.5616627 at 80iterations 8.5675791E-03 0.2764874 at 90iterations 3.9311084E-03 0.1196532 at 100iterations 1.8176473E-03 5.8724880E-02 at 110iterations 8.5033674E-04 2.7595520E-02 at 120iterations finished qdiffx linear iterations at : 13:38:42 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 8.5033674E-04 2.7595520E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 13:38:43 9.482u 0.303s 0:19.09 51.2% 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 Sat Oct 15 2011 at 13:38:43 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3335 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLU 207 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.685622 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): -12.93900 45.12000 ymin,ymax (A): -9.030000 50.62100 zmin,zma (A): -14.07100 39.87600 x,y,z range (A): 58.05900 59.65100 53.94700 scale (grids/A): 2.685622 object centre (A): 16.09050 20.79550 12.90250 number of atom coordinates read : 3335 total number of charged atoms : 3190 net assigned charge : -6.599979 assigned positive charge : 510.4935 centred at (gu) : 90.55225 91.11829 89.23495 assigned negative charge : -517.0945 centred at (gu) : 90.67083 91.70864 89.65624 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 199538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32390 grid for indexing accessible points = 1.400000 m= 94748 mr = 140143 m= 30502 mr = 73940 m= 6398 mr = 22837 m= 685 mr = 4416 m= 24 mr = 372 m= 0 mr = 2 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 11313 time to turn everything in is 1.140000 number of dielectric boundary points 90185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 25507 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) : 1.790414 object centre at (A) : 16.09050 20.79550 12.90250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1293566 1.7142717E-02 midg,1,midg; midg,igrid,midg 4.0748425E-02 -0.1954882 1,midg,midg; igrid,midg,midg 0.2191170 -0.3544730 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 1.440000 now iterating at: 13:38:46 rms-change max change #iterations 11.01170 298.9682 at 10iterations 6.614577 185.4473 at 20iterations 3.919113 93.97115 at 30iterations 2.319339 58.26931 at 40iterations 1.363772 28.95857 at 50iterations 0.8022299 18.56643 at 60iterations 0.4682580 8.610649 at 70iterations 0.2741752 5.180435 at 80iterations 0.1601283 3.099748 at 90iterations 9.3158610E-02 1.822714 at 100iterations 5.4194763E-02 1.087118 at 110iterations 3.1459466E-02 0.6092415 at 120iterations 1.8303692E-02 0.3408375 at 130iterations 1.0619886E-02 0.1999645 at 140iterations 6.1712377E-03 0.1214294 at 150iterations 3.5854930E-03 6.1752796E-02 at 160iterations 2.0891402E-03 4.0149689E-02 at 170iterations 1.2211867E-03 2.4424076E-02 at 180iterations finished qdiffx linear iterations at : 13:39:04 total time elapsed so far: 14.41000 # loops : 180 mean,max change (kT/e) : 1.2211867E-03 2.4424076E-02 energy calculations done at 14.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.55000 DelPhi exited at 13:39:05 14.551u 0.266s 0:22.17 66.8% 0+0k 0+0io 0pf+0w