Sat Oct 8 20:17:34 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 20:17:34 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 460 has a net charge of 1.4000 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: 0.6182702 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): -31.34800 17.54800 ymin,ymax (A): -23.10400 22.51700 zmin,zma (A): -12.33000 45.25000 x,y,z range (A): 48.89600 45.62100 57.58000 scale (grids/A): 0.6182702 object centre (A): -6.900000 -0.2934999 16.46000 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.44185 89.24712 89.56775 assigned negative charge : -387.9385 centred at (gu) : 88.34916 89.28916 89.44866 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6416 nv = 96 ne = 84 npr = 54327 no. pairs analyzed = 54327 no. exposed pairs = 2963 no. arc points = 21337 no. surface atoms = 1006 nbur = 1588 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 323 mr = 3603 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.2900000 number of dielectric boundary points 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8022 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9797730E-09 9.5381099E-09 midg,1,midg; midg,igrid,midg 6.7640142E-09 3.9218426E-10 1,midg,midg; igrid,midg,midg -4.0698480E-09 6.3068155E-09 gauss-seidel spectral radius is 0.9864472 estimated iterations to convergence 70 setup time was (sec) 0.5700000 now iterating at: 20:17:35 rms-change max change #iterations 0.1268835 19.85246 at 10iterations 1.1398186E-02 1.746861 at 20iterations 1.0687573E-03 0.1431007 at 30iterations 1.0197193E-04 1.4091492E-02 at 40iterations 9.7369111E-06 1.5029907E-03 at 50iterations finished qdiffx linear iterations at : 20:17:39 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 9.7369111E-06 1.5029907E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 20:17:39 4.163u 0.246s 0:04.70 93.6% 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 Sat Oct 8 2011 at 20:17:39 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 460 has a net charge of 1.4000 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: 1.854811 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): -31.34800 17.54800 ymin,ymax (A): -23.10400 22.51700 zmin,zma (A): -12.33000 45.25000 x,y,z range (A): 48.89600 45.62100 57.58000 scale (grids/A): 1.854811 object centre (A): -6.900000 -0.2934999 16.46000 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.32485 87.74079 88.70285 assigned negative charge : -387.9385 centred at (gu) : 85.04708 87.86723 88.34573 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21337 grid for indexing accessible points = 1.400000 m= 24038 mr = 49523 m= 3481 mr = 17737 m= 175 mr = 2189 m= 0 mr = 48 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5616 time to turn everything in is 0.5200000 number of dielectric boundary points 28480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19231 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) : 0.6182702 object centre at (A) : -6.900000 -0.2934999 16.46000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3952257E-02 2.0571139E-02 midg,1,midg; midg,igrid,midg 1.1234474E-02 2.2828367E-03 1,midg,midg; igrid,midg,midg -1.9963530E-03 2.8986087E-02 gauss-seidel spectral radius is 0.9985565 estimated iterations to convergence 209 setup time was (sec) 0.8400000 now iterating at: 20:17:40 rms-change max change #iterations 4.001336 152.4385 at 10iterations 1.840215 72.59177 at 20iterations 0.8385932 29.46235 at 30iterations 0.3850271 15.23099 at 40iterations 0.1769823 6.053196 at 50iterations 8.1086375E-02 2.609178 at 60iterations 3.7328646E-02 1.570917 at 70iterations 1.7084643E-02 0.5384464 at 80iterations 7.8411298E-03 0.2575331 at 90iterations 3.5908662E-03 0.1173692 at 100iterations 1.6492567E-03 5.0055504E-02 at 110iterations 7.5881660E-04 2.6359558E-02 at 120iterations finished qdiffx linear iterations at : 20:17:49 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 7.5881660E-04 2.6359558E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 20:17:49 9.438u 0.292s 0:09.99 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 20:17:49 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 460 has a net charge of 1.4000 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: 2.782216 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): -31.34800 17.54800 ymin,ymax (A): -23.10400 22.51700 zmin,zma (A): -12.33000 45.25000 x,y,z range (A): 48.89600 45.62100 57.58000 scale (grids/A): 2.782216 object centre (A): -6.900000 -0.2934999 16.46000 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 82.98721 86.61120 88.05408 assigned negative charge : -387.9385 centred at (gu) : 82.57058 86.80086 87.51852 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 162769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21337 grid for indexing accessible points = 1.400000 m= 79878 mr = 119572 m= 27089 mr = 65890 m= 6253 mr = 21813 m= 768 mr = 4715 m= 36 mr = 501 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 18371 time to turn everything in is 1.330000 number of dielectric boundary points 64285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 19598 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) : 1.854811 object centre at (A) : -6.900000 -0.2934999 16.46000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5377906E-02 0.2525793 midg,1,midg; midg,igrid,midg 0.1405248 1.2233952E-03 1,midg,midg; igrid,midg,midg -2.5504734E-02 0.3882994 gauss-seidel spectral radius is 0.9992298 estimated iterations to convergence 284 setup time was (sec) 1.670000 now iterating at: 20:17:51 rms-change max change #iterations 9.407839 387.0422 at 10iterations 5.402661 142.9195 at 20iterations 3.086620 64.33835 at 30iterations 1.757974 54.00841 at 40iterations 0.9996635 20.31856 at 50iterations 0.5697258 12.59101 at 60iterations 0.3236640 6.442710 at 70iterations 0.1840880 3.677140 at 80iterations 0.1045761 1.998251 at 90iterations 5.9492122E-02 1.530765 at 100iterations 3.3814866E-02 0.7272410 at 110iterations 1.9203523E-02 0.3576488 at 120iterations 1.0912666E-02 0.2051926 at 130iterations 6.2072175E-03 0.1170740 at 140iterations 3.5272618E-03 6.7199707E-02 at 150iterations 1.9990269E-03 3.6352634E-02 at 160iterations 1.1380594E-03 2.1112442E-02 at 170iterations 6.4837816E-04 1.2395859E-02 at 180iterations finished qdiffx linear iterations at : 20:18:04 total time elapsed so far: 15.14000 # loops : 180 mean,max change (kT/e) : 6.4837816E-04 1.2395859E-02 energy calculations done at 15.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 20:18:05 15.324u 0.291s 0:15.88 98.2% 0+0k 0+0io 0pf+0w