Sat Oct 8 21:02:36 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 21:02:36 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! 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 444 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6179376 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): -31.35400 17.19400 ymin,ymax (A): -23.11400 23.83400 zmin,zma (A): -12.56900 45.04200 x,y,z range (A): 48.54800 46.94800 57.61100 scale (grids/A): 0.6179376 object centre (A): -7.080000 0.3599997 16.23650 number of atom coordinates read : 2600 total number of charged atoms : 2457 net assigned charge : 3.906009 assigned positive charge : 393.8021 centred at (gu) : 88.59309 88.82492 89.77158 assigned negative charge : -389.8965 centred at (gu) : 88.50584 88.86415 89.63815 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6441 nv = 96 ne = 84 npr = 54548 no. pairs analyzed = 54548 no. exposed pairs = 2990 no. arc points = 21281 no. surface atoms = 1013 nbur = 1587 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3618 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.1900000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7570100E-09 1.0704711E-08 midg,1,midg; midg,igrid,midg 7.0915314E-09 4.6000415E-10 1,midg,midg; igrid,midg,midg -3.5035743E-09 6.2001844E-09 gauss-seidel spectral radius is 0.9864333 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 21:02:36 rms-change max change #iterations 0.1276966 20.69218 at 10iterations 1.1715953E-02 2.022615 at 20iterations 1.0846757E-03 0.1722050 at 30iterations 1.0784214E-04 2.0187378E-02 at 40iterations 1.1240732E-05 1.9969940E-03 at 50iterations finished qdiffx linear iterations at : 21:02:39 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1240732E-05 1.9969940E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 21:02:40 3.352u 0.182s 0:03.91 90.2% 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 21:02:40 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! 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 444 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.853813 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): -31.35400 17.19400 ymin,ymax (A): -23.11400 23.83400 zmin,zma (A): -12.56900 45.04200 x,y,z range (A): 48.54800 46.94800 57.61100 scale (grids/A): 1.853813 object centre (A): -7.080000 0.3599997 16.23650 number of atom coordinates read : 2600 total number of charged atoms : 2457 net assigned charge : 3.906009 assigned positive charge : 393.8021 centred at (gu) : 85.77896 86.47443 89.31435 assigned negative charge : -389.8965 centred at (gu) : 85.51746 86.59215 88.91411 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21281 grid for indexing accessible points = 1.400000 m= 24227 mr = 49555 m= 3417 mr = 17816 m= 142 mr = 1998 m= 4 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3744 time to turn everything in is 0.3600000 number of dielectric boundary points 28720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19249 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) : 0.6179376 object centre at (A) : -7.080000 0.3599997 16.23650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2824399E-02 2.2734705E-02 midg,1,midg; midg,igrid,midg 1.4627986E-02 3.7945230E-03 1,midg,midg; igrid,midg,midg -1.1482828E-03 2.8787121E-02 gauss-seidel spectral radius is 0.9985546 estimated iterations to convergence 209 setup time was (sec) 0.5900000 now iterating at: 21:02:41 rms-change max change #iterations 4.037391 194.1974 at 10iterations 1.858813 65.09306 at 20iterations 0.8510323 28.05073 at 30iterations 0.3881744 13.37961 at 40iterations 0.1788000 5.595634 at 50iterations 8.2336463E-02 2.596344 at 60iterations 3.7657958E-02 1.300611 at 70iterations 1.7253883E-02 0.6215878 at 80iterations 7.9090865E-03 0.2695675 at 90iterations 3.6393648E-03 0.1409264 at 100iterations 1.6656002E-03 5.8292389E-02 at 110iterations 7.6636946E-04 2.4892569E-02 at 120iterations finished qdiffx linear iterations at : 21:02:48 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 7.6636946E-04 2.4892569E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 21:02:49 7.744u 0.937s 0:09.11 95.1% 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 21:02:49 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! 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 444 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.780719 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): -31.35400 17.19400 ymin,ymax (A): -23.11400 23.83400 zmin,zma (A): -12.56900 45.04200 x,y,z range (A): 48.54800 46.94800 57.61100 scale (grids/A): 2.780719 object centre (A): -7.080000 0.3599997 16.23650 number of atom coordinates read : 2600 total number of charged atoms : 2457 net assigned charge : 3.906009 assigned positive charge : 393.8021 centred at (gu) : 83.66839 84.71146 88.97143 assigned negative charge : -389.8965 centred at (gu) : 83.27618 84.88813 88.37120 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21281 grid for indexing accessible points = 1.400000 m= 80603 mr = 119858 m= 26977 mr = 66464 m= 6099 mr = 21432 m= 620 mr = 4464 m= 20 mr = 324 m= 0 mr = 7 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 12700 time to turn everything in is 0.8700000 number of dielectric boundary points 64722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19652 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) : 1.853813 object centre at (A) : -7.080000 0.3599997 16.23650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1355077 0.2441648 midg,1,midg; midg,igrid,midg 0.1593128 1.1335667E-02 1,midg,midg; igrid,midg,midg 2.1386564E-02 0.3671082 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.090000 now iterating at: 21:02:50 rms-change max change #iterations 9.523751 452.1496 at 10iterations 5.467284 116.9120 at 20iterations 3.130022 74.25912 at 30iterations 1.780804 35.73085 at 40iterations 1.015096 22.06234 at 50iterations 0.5787272 11.67297 at 60iterations 0.3289253 7.023705 at 70iterations 0.1873438 3.954881 at 80iterations 0.1064988 2.115232 at 90iterations 6.0379345E-02 1.186806 at 100iterations 3.4336291E-02 0.6835136 at 110iterations 1.9516321E-02 0.4156532 at 120iterations 1.1116765E-02 0.2233505 at 130iterations 6.3174707E-03 0.1159439 at 140iterations 3.5881477E-03 7.1455002E-02 at 150iterations 2.0501614E-03 4.1284561E-02 at 160iterations 1.1678515E-03 2.3718834E-02 at 170iterations 6.6845445E-04 1.3330460E-02 at 180iterations finished qdiffx linear iterations at : 21:03:02 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 6.6845445E-04 1.3330460E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 21:03:03 12.262u 1.529s 0:14.06 98.0% 0+0k 0+0io 0pf+0w