Sat Oct 8 17:49:02 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 17:49:02 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 = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5222468 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): 41.21800 109.3850 ymin,ymax (A): 10.32300 56.99900 zmin,zma (A): 2.670000 51.21100 x,y,z range (A): 68.16701 46.67599 48.54100 scale (grids/A): 0.5222468 object centre (A): 75.30150 33.66100 26.94050 number of atom coordinates read : 3305 total number of charged atoms : 3162 net assigned charge : -0.9999939 assigned positive charge : 497.1877 centred at (gu) : 90.26746 88.86177 90.24339 assigned negative charge : -498.1890 centred at (gu) : 90.28162 88.74100 90.23547 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5828 nv = 96 ne = 84 npr = 66778 no. pairs analyzed = 66778 no. exposed pairs = 4053 no. arc points = 27911 no. surface atoms = 1363 nbur = 1942 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 199 mr = 3059 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2837 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 7664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9530705E-11 4.8779526E-12 midg,1,midg; midg,igrid,midg -5.1231919E-10 2.4574964E-10 1,midg,midg; igrid,midg,midg 2.1219386E-11 -6.4811927E-11 gauss-seidel spectral radius is 0.9811361 estimated iterations to convergence 60 setup time was (sec) 0.7800000 now iterating at: 17:49:04 rms-change max change #iterations 6.1335504E-02 18.60992 at 10iterations 3.6453232E-03 0.8316650 at 20iterations 2.6595773E-04 5.1858902E-02 at 30iterations 4.0348317E-05 7.7601671E-03 at 40iterations 9.4598345E-06 1.8553734E-03 at 50iterations finished qdiffx linear iterations at : 17:49:07 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 9.4598345E-06 1.8553734E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 17:49:08 4.624u 0.433s 0:05.36 94.2% 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 8 2011 at 17:49:08 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 = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.566740 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): 41.21800 109.3850 ymin,ymax (A): 10.32300 56.99900 zmin,zma (A): 2.670000 51.21100 x,y,z range (A): 68.16701 46.67599 48.54100 scale (grids/A): 1.566740 object centre (A): 75.30150 33.66100 26.94050 number of atom coordinates read : 3305 total number of charged atoms : 3162 net assigned charge : -0.9999939 assigned positive charge : 497.1877 centred at (gu) : 90.80138 86.58437 90.72968 assigned negative charge : -498.1890 centred at (gu) : 90.84434 86.22277 90.70602 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19853 mr = 45360 m= 1775 mr = 13424 m= 47 mr = 729 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 0.6700000 number of dielectric boundary points 27414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23962 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) : 0.5222468 object centre at (A) : 75.30150 33.66100 26.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9742334E-03 -4.1849300E-04 midg,1,midg; midg,igrid,midg -6.7125405E-03 4.6539097E-03 1,midg,midg; igrid,midg,midg 8.8499105E-03 -3.2175572E-03 gauss-seidel spectral radius is 0.9980476 estimated iterations to convergence 180 setup time was (sec) 0.9900000 now iterating at: 17:49:09 rms-change max change #iterations 3.220379 146.9559 at 10iterations 1.298540 61.03618 at 20iterations 0.5241759 21.44815 at 30iterations 0.2124244 7.852640 at 40iterations 8.6024620E-02 3.072330 at 50iterations 3.4643557E-02 1.301807 at 60iterations 1.4069825E-02 0.5329535 at 70iterations 5.6844694E-03 0.2013931 at 80iterations 2.3152006E-03 8.4758759E-02 at 90iterations 9.4525382E-04 3.9505005E-02 at 100iterations 3.9446927E-04 1.5262127E-02 at 110iterations 1.6906092E-04 6.8005323E-03 at 120iterations finished qdiffx linear iterations at : 17:49:18 total time elapsed so far: 9.780000 # loops : 120 mean,max change (kT/e) : 1.6906092E-04 6.8005323E-03 energy calculations done at 9.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 17:49:19 10.005u 0.458s 0:10.75 97.2% 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 8 2011 at 17:49:19 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 = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.350111 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): 41.21800 109.3850 ymin,ymax (A): 10.32300 56.99900 zmin,zma (A): 2.670000 51.21100 x,y,z range (A): 68.16701 46.67599 48.54100 scale (grids/A): 2.350111 object centre (A): 75.30150 33.66100 26.94050 number of atom coordinates read : 3305 total number of charged atoms : 3162 net assigned charge : -0.9999939 assigned positive charge : 497.1877 centred at (gu) : 91.20200 84.87621 91.09435 assigned negative charge : -498.1890 centred at (gu) : 91.26643 84.33409 91.05891 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 151929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 70125 mr = 111073 m= 18674 mr = 55383 m= 2605 mr = 13537 m= 154 mr = 1508 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 1996 time to turn everything in is 1.650000 number of dielectric boundary points 61945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 25250 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) : 1.566740 object centre at (A) : 75.30150 33.66100 26.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2527052E-02 -9.0947198E-03 midg,1,midg; midg,igrid,midg -9.9867001E-02 8.1170097E-02 1,midg,midg; igrid,midg,midg 0.4854920 -0.1162487 gauss-seidel spectral radius is 0.9990973 estimated iterations to convergence 263 setup time was (sec) 2.000000 now iterating at: 17:49:21 rms-change max change #iterations 8.465087 250.8366 at 10iterations 4.678958 113.5696 at 20iterations 2.574622 58.56895 at 30iterations 1.415014 36.60998 at 40iterations 0.7726253 17.24729 at 50iterations 0.4215347 10.14104 at 60iterations 0.2299782 4.619410 at 70iterations 0.1248667 2.514808 at 80iterations 6.7831926E-02 1.338602 at 90iterations 3.6840469E-02 0.7830663 at 100iterations 1.9979978E-02 0.4002371 at 110iterations 1.0858888E-02 0.2338114 at 120iterations 5.8908323E-03 0.1204205 at 130iterations 3.2001818E-03 7.2692394E-02 at 140iterations 1.7319440E-03 3.9096832E-02 at 150iterations 9.3866838E-04 2.2434235E-02 at 160iterations 5.0928106E-04 1.1295319E-02 at 170iterations 2.7687510E-04 5.8393478E-03 at 180iterations finished qdiffx linear iterations at : 17:49:36 total time elapsed so far: 16.40000 # loops : 180 mean,max change (kT/e) : 2.7687510E-04 5.8393478E-03 energy calculations done at 16.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.64000 DelPhi exited at 17:49:36 16.642u 0.472s 0:17.51 97.7% 0+0k 0+0io 0pf+0w