Wed Dec 21 14:21:33 PST 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 Wed Dec 21 2011 at 14:21:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5756419 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): -35.30900 10.04900 ymin,ymax (A): 1.237000 41.30400 zmin,zma (A): -2.707000 59.13700 x,y,z range (A): 45.35800 40.06700 61.84400 scale (grids/A): 0.5756419 object centre (A): -12.63000 21.27050 28.21500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.0260 centred at (gu) : 90.38444 89.58395 89.72547 assigned negative charge : -289.0262 centred at (gu) : 90.32554 89.73820 89.71603 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4381 nv = 96 ne = 84 npr = 40130 no. pairs analyzed = 40130 no. exposed pairs = 2402 no. arc points = 16784 no. surface atoms = 826 nbur = 1138 mkacc time = 7.0000008E-02 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 = 1.512000 m= 166 mr = 2396 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1756 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 5463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6398891E-10 4.5251175E-10 midg,1,midg; midg,igrid,midg 2.4743632E-09 -1.4288671E-09 1,midg,midg; igrid,midg,midg -3.3514638E-10 1.1933166E-09 gauss-seidel spectral radius is 0.9843424 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 14:21:36 rms-change max change #iterations 7.8286596E-02 13.98158 at 10iterations 5.9469948E-03 1.235138 at 20iterations 4.5538609E-04 8.0486298E-02 at 30iterations 3.4183584E-05 6.1120987E-03 at 40iterations 2.6017406E-06 4.6157837E-04 at 50iterations finished qdiffx linear iterations at : 14:21:41 total time elapsed so far: 5.370000 # loops : 50 mean,max change (kT/e) : 2.6017406E-06 4.6157837E-04 energy calculations done at 5.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.510000 DelPhi exited at 14:21:46 5.513u 0.574s 0:13.32 45.6% 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 Wed Dec 21 2011 at 14:21:51 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.726926 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): -35.30900 10.04900 ymin,ymax (A): 1.237000 41.30400 zmin,zma (A): -2.707000 59.13700 x,y,z range (A): 45.35800 40.06700 61.84400 scale (grids/A): 1.726926 object centre (A): -12.63000 21.27050 28.21500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.0260 centred at (gu) : 91.15359 88.75189 89.17640 assigned negative charge : -289.0262 centred at (gu) : 90.97686 89.21464 89.14834 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 47947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16784 grid for indexing accessible points = 1.400000 m= 16533 mr = 33009 m= 2006 mr = 12404 m= 68 mr = 1170 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 403 time to turn everything in is 0.2700000 number of dielectric boundary points 19959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14213 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) : 0.5756419 object centre at (A) : -12.63000 21.27050 28.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9818466E-02 1.8619251E-02 midg,1,midg; midg,igrid,midg 1.9362060E-03 -8.5825920E-03 1,midg,midg; igrid,midg,midg -2.2838085E-03 -1.6377784E-03 gauss-seidel spectral radius is 0.9982618 estimated iterations to convergence 190 setup time was (sec) 0.4900000 now iterating at: 14:21:53 rms-change max change #iterations 3.004990 153.4795 at 10iterations 1.265811 51.82157 at 20iterations 0.5391967 23.79400 at 30iterations 0.2280663 8.921776 at 40iterations 9.7381689E-02 3.734611 at 50iterations 4.1333959E-02 1.619995 at 60iterations 1.7589020E-02 0.7153883 at 70iterations 7.4570733E-03 0.2900333 at 80iterations 3.1804703E-03 0.1390725 at 90iterations 1.3518730E-03 5.3448677E-02 at 100iterations 5.7488034E-04 2.2418976E-02 at 110iterations 2.4399743E-04 9.8009109E-03 at 120iterations finished qdiffx linear iterations at : 14:22:00 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.4399743E-04 9.8009109E-03 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:22:12 7.724u 0.208s 0:20.69 38.2% 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 Wed Dec 21 2011 at 14:22:14 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.590389 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): -35.30900 10.04900 ymin,ymax (A): 1.237000 41.30400 zmin,zma (A): -2.707000 59.13700 x,y,z range (A): 45.35800 40.06700 61.84400 scale (grids/A): 2.590389 object centre (A): -12.63000 21.27050 28.21500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.0260 centred at (gu) : 91.73044 88.12784 88.76459 assigned negative charge : -289.0262 centred at (gu) : 91.46531 88.82195 88.72247 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 110896 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16784 grid for indexing accessible points = 1.400000 m= 55225 mr = 79892 m= 17942 mr = 45548 m= 3337 mr = 14686 m= 310 mr = 2376 m= 9 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1262 time to turn everything in is 0.6300000 number of dielectric boundary points 45018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14642 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) : 1.726926 object centre at (A) : -12.63000 21.27050 28.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1515885 0.1445622 midg,1,midg; midg,igrid,midg -8.8667562E-03 -0.1167663 1,midg,midg; igrid,midg,midg -4.5987993E-02 -4.4927709E-02 gauss-seidel spectral radius is 0.9991273 estimated iterations to convergence 267 setup time was (sec) 0.8800000 now iterating at: 14:22:19 rms-change max change #iterations 7.331095 276.4462 at 10iterations 4.063962 130.7180 at 20iterations 2.235288 55.73830 at 30iterations 1.228348 30.74453 at 40iterations 0.6739064 15.93637 at 50iterations 0.3676995 9.681894 at 60iterations 0.2014100 5.306107 at 70iterations 0.1100406 2.542287 at 80iterations 6.0178120E-02 1.472923 at 90iterations 3.2876439E-02 0.7671642 at 100iterations 1.7952546E-02 0.3828378 at 110iterations 9.8198196E-03 0.2248211 at 120iterations 5.3633885E-03 0.1403809 at 130iterations 2.9325914E-03 7.4567795E-02 at 140iterations 1.6012623E-03 3.6052346E-02 at 150iterations 8.7546388E-04 2.0238876E-02 at 160iterations 4.7740611E-04 1.1374235E-02 at 170iterations 2.6082396E-04 6.1702728E-03 at 180iterations finished qdiffx linear iterations at : 14:22:33 total time elapsed so far: 14.95000 # loops : 180 mean,max change (kT/e) : 2.6082396E-04 6.1702728E-03 energy calculations done at 14.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 14:22:48 15.080u 0.296s 0:33.85 45.4% 0+0k 0+0io 0pf+0w