Sat Oct 8 14:23:24 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 14:23:25 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6014834 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): -27.07800 23.49300 ymin,ymax (A): -34.84000 24.34700 zmin,zma (A): -27.75500 24.67600 x,y,z range (A): 50.57100 59.18700 52.43100 scale (grids/A): 0.6014834 object centre (A): -1.792500 -5.246500 -1.539501 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 1.4008060E-02 assigned positive charge : 456.1556 centred at (gu) : 91.45856 92.11507 91.13193 assigned negative charge : -456.1423 centred at (gu) : 91.50800 92.02719 91.20035 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7072 nv = 96 ne = 84 npr = 64313 no. pairs analyzed = 64313 no. exposed pairs = 3457 no. arc points = 24048 no. surface atoms = 1173 nbur = 1862 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 4074 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3300000 number of dielectric boundary points 3295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2442 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9056 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3237607E-09 -4.0024264E-09 midg,1,midg; midg,igrid,midg -2.4440121E-09 6.3292824E-09 1,midg,midg; igrid,midg,midg 1.5608020E-09 -3.1186917E-09 gauss-seidel spectral radius is 0.9857204 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 14:23:25 rms-change max change #iterations 0.1219167 18.12602 at 10iterations 1.0413332E-02 1.500488 at 20iterations 9.8314194E-04 0.1388445 at 30iterations 1.1298393E-04 1.6208172E-02 at 40iterations 1.8635526E-05 2.5577545E-03 at 50iterations finished qdiffx linear iterations at : 14:23:28 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.8635526E-05 2.5577545E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 14:23:29 3.479u 0.227s 0:04.04 91.3% 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 14:23:29 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.804450 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): -27.07800 23.49300 ymin,ymax (A): -34.84000 24.34700 zmin,zma (A): -27.75500 24.67600 x,y,z range (A): 50.57100 59.18700 52.43100 scale (grids/A): 1.804450 object centre (A): -1.792500 -5.246500 -1.539501 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 1.4008060E-02 assigned positive charge : 456.1556 centred at (gu) : 94.37515 96.34477 93.39524 assigned negative charge : -456.1423 centred at (gu) : 94.52364 96.08112 93.60087 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 26520 mr = 56197 m= 3260 mr = 19524 m= 123 mr = 1853 m= 0 mr = 25 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 101 time to turn everything in is 0.5500000 number of dielectric boundary points 30581 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22574 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) : 0.6014834 object centre at (A) : -1.792500 -5.246500 -1.539501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3124815E-02 8.9226533E-03 midg,1,midg; midg,igrid,midg -1.3204166E-02 3.2148082E-02 1,midg,midg; igrid,midg,midg 4.0930966E-03 -1.1695485E-02 gauss-seidel spectral radius is 0.9985136 estimated iterations to convergence 206 setup time was (sec) 0.8600000 now iterating at: 14:23:30 rms-change max change #iterations 4.191213 162.9624 at 10iterations 1.901171 63.35770 at 20iterations 0.8623338 26.82680 at 30iterations 0.3928511 12.05881 at 40iterations 0.1777857 6.291683 at 50iterations 8.0759048E-02 2.622874 at 60iterations 3.6702625E-02 1.306595 at 70iterations 1.6730884E-02 0.5273075 at 80iterations 7.6098186E-03 0.2431793 at 90iterations 3.4594457E-03 0.1069878 at 100iterations 1.5780823E-03 5.2109718E-02 at 110iterations 7.2285754E-04 2.3056030E-02 at 120iterations finished qdiffx linear iterations at : 14:23:37 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 7.2285754E-04 2.3056030E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 14:23:37 8.114u 0.243s 0:08.68 96.1% 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 Sat Oct 8 2011 at 14:23:37 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3035 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.706676 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): -27.07800 23.49300 ymin,ymax (A): -34.84000 24.34700 zmin,zma (A): -27.75500 24.67600 x,y,z range (A): 50.57100 59.18700 52.43100 scale (grids/A): 2.706676 object centre (A): -1.792500 -5.246500 -1.539501 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 1.4008060E-02 assigned positive charge : 456.1556 centred at (gu) : 96.56280 99.51707 95.09286 assigned negative charge : -456.1423 centred at (gu) : 96.78545 99.12170 95.40119 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 181676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 89676 mr = 136363 m= 28645 mr = 73881 m= 5492 mr = 22650 m= 538 mr = 3909 m= 7 mr = 292 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 1.380000 number of dielectric boundary points 68939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 23099 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) : 1.804450 object centre at (A) : -1.792500 -5.246500 -1.539501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1443035 0.2314139 midg,1,midg; midg,igrid,midg -9.1575868E-02 0.4492612 1,midg,midg; igrid,midg,midg 7.1761049E-02 -7.8444667E-02 gauss-seidel spectral radius is 0.9992276 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 14:23:39 rms-change max change #iterations 10.00641 330.7753 at 10iterations 5.774366 125.8615 at 20iterations 3.305441 67.77718 at 30iterations 1.890401 34.11372 at 40iterations 1.078871 21.27734 at 50iterations 0.6160739 13.17338 at 60iterations 0.3510036 7.069300 at 70iterations 0.1998465 3.559683 at 80iterations 0.1136699 1.995966 at 90iterations 6.4584069E-02 1.174610 at 100iterations 3.6731075E-02 0.6661081 at 110iterations 2.0832472E-02 0.4149055 at 120iterations 1.1889634E-02 0.2259941 at 130iterations 6.7619644E-03 0.1189690 at 140iterations 3.8400434E-03 6.8080902E-02 at 150iterations 2.1934849E-03 3.9258957E-02 at 160iterations 1.2480414E-03 2.1857738E-02 at 170iterations 7.1603956E-04 1.2413025E-02 at 180iterations finished qdiffx linear iterations at : 14:23:50 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 7.1603956E-04 1.2413025E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 14:23:51 13.016u 0.261s 0:13.57 97.7% 0+0k 0+0io 0pf+0w