Sat Oct 15 14:18:46 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 14:18:46 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5103943 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): -18.54000 37.18900 ymin,ymax (A): -30.72100 34.14100 zmin,zma (A): -4.083000 65.66700 x,y,z range (A): 55.72900 64.86200 69.75000 scale (grids/A): 0.5103943 object centre (A): 9.324502 1.710001 30.79200 number of atom coordinates read : 4812 total number of charged atoms : 4561 net assigned charge : 6.706030 assigned positive charge : 723.2145 centred at (gu) : 90.20464 90.52515 88.45606 assigned negative charge : -716.5128 centred at (gu) : 90.09288 90.59886 88.43678 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8007 nv = 96 ne = 84 npr = 96617 no. pairs analyzed = 96617 no. exposed pairs = 6080 no. arc points = 42849 no. surface atoms = 2037 nbur = 2775 mkacc time = 0.1700000 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 = 1.680000 m= 275 mr = 4116 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4123 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10594 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6936845E-11 9.7403800E-11 midg,1,midg; midg,igrid,midg 2.4673236E-10 -1.1111852E-10 1,midg,midg; igrid,midg,midg -1.8554723E-10 3.9984216E-10 gauss-seidel spectral radius is 0.9803746 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 14:18:46 rms-change max change #iterations 6.6832080E-02 11.50602 at 10iterations 3.9248881E-03 0.5765038 at 20iterations 3.8407228E-04 5.3758621E-02 at 30iterations 1.1739176E-04 1.7965555E-02 at 40iterations 4.6305198E-05 7.2808266E-03 at 50iterations finished qdiffx linear iterations at : 14:18:49 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 4.6305198E-05 7.2808266E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:18:50 3.734u 0.216s 0:04.27 92.2% 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 14:18:50 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.531183 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): -18.54000 37.18900 ymin,ymax (A): -30.72100 34.14100 zmin,zma (A): -4.083000 65.66700 x,y,z range (A): 55.72900 64.86200 69.75000 scale (grids/A): 1.531183 object centre (A): 9.324502 1.710001 30.79200 number of atom coordinates read : 4812 total number of charged atoms : 4561 net assigned charge : 6.706030 assigned positive charge : 723.2145 centred at (gu) : 90.61250 91.57379 85.36686 assigned negative charge : -716.5128 centred at (gu) : 90.27842 91.79620 85.31014 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 90805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42849 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25955 mr = 62297 m= 2188 mr = 16996 m= 49 mr = 873 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.4500000 number of dielectric boundary points 38829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 578 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 34331 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) : 0.5103943 object centre at (A) : 9.324502 1.710001 30.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1784727E-03 2.0594699E-02 midg,1,midg; midg,igrid,midg 1.2968513E-02 -1.4237535E-02 1,midg,midg; igrid,midg,midg -1.7433849E-03 1.1649708E-02 gauss-seidel spectral radius is 0.9981186 estimated iterations to convergence 183 setup time was (sec) 0.7000000 now iterating at: 14:18:51 rms-change max change #iterations 3.788970 167.8947 at 10iterations 1.550896 48.40188 at 20iterations 0.6374686 19.45090 at 30iterations 0.2615931 8.457555 at 40iterations 0.1073979 3.418782 at 50iterations 4.4328630E-02 1.384384 at 60iterations 1.8190080E-02 0.6071091 at 70iterations 7.4948743E-03 0.2437019 at 80iterations 3.1007605E-03 0.1015053 at 90iterations 1.2781803E-03 4.2850494E-02 at 100iterations 5.3417240E-04 1.7120361E-02 at 110iterations 2.3054378E-04 8.0261230E-03 at 120iterations finished qdiffx linear iterations at : 14:18:59 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 2.3054378E-04 8.0261230E-03 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 14:18:59 8.514u 0.229s 0:09.01 96.8% 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 14:18:59 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.296774 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): -18.54000 37.18900 ymin,ymax (A): -30.72100 34.14100 zmin,zma (A): -4.083000 65.66700 x,y,z range (A): 55.72900 64.86200 69.75000 scale (grids/A): 2.296774 object centre (A): 9.324502 1.710001 30.79200 number of atom coordinates read : 4812 total number of charged atoms : 4561 net assigned charge : 6.706030 assigned positive charge : 723.2145 centred at (gu) : 90.91838 92.36021 83.04999 assigned negative charge : -716.5128 centred at (gu) : 90.41746 92.69424 82.96521 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 211632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42849 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93699 mr = 153181 m= 23164 mr = 72681 m= 3065 mr = 16339 m= 173 mr = 1763 m= 0 mr = 78 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 557 time to turn everything in is 1.100000 number of dielectric boundary points 87691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 36375 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) : 1.531183 object centre at (A) : 9.324502 1.710001 30.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1592344 0.5051044 midg,1,midg; midg,igrid,midg 0.2486830 -0.3067342 1,midg,midg; igrid,midg,midg -1.4957392E-02 0.1691820 gauss-seidel spectral radius is 0.9991662 estimated iterations to convergence 274 setup time was (sec) 1.370000 now iterating at: 14:19:01 rms-change max change #iterations 10.35481 310.8551 at 10iterations 5.932997 141.1587 at 20iterations 3.383057 75.76132 at 30iterations 1.912241 44.18965 at 40iterations 1.078983 21.10079 at 50iterations 0.6078235 13.09130 at 60iterations 0.3416606 7.282980 at 70iterations 0.1911039 3.851037 at 80iterations 0.1069026 2.209648 at 90iterations 5.9727732E-02 1.140139 at 100iterations 3.3312280E-02 0.6897039 at 110iterations 1.8596988E-02 0.3485374 at 120iterations 1.0362088E-02 0.2080460 at 130iterations 5.7741208E-03 0.1223316 at 140iterations 3.2247591E-03 6.0025215E-02 at 150iterations 1.8010664E-03 3.4113884E-02 at 160iterations 1.0120593E-03 1.9813538E-02 at 170iterations 5.7539815E-04 1.1676788E-02 at 180iterations finished qdiffx linear iterations at : 14:19:13 total time elapsed so far: 14.03000 # loops : 180 mean,max change (kT/e) : 5.7539815E-04 1.1676788E-02 energy calculations done at 14.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.17000 DelPhi exited at 14:19:14 14.169u 0.244s 0:14.69 98.0% 0+0k 0+0io 0pf+0w