Tue Oct 11 06:01:59 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 Tue Oct 11 2011 at 06:02:00 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7346568 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): 25.62500 72.11100 ymin,ymax (A): -18.59700 29.86100 zmin,zma (A): 4.167000 46.30400 x,y,z range (A): 46.48600 48.45800 42.13700 scale (grids/A): 0.7346568 object centre (A): 48.86800 5.632000 25.23550 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 317.9760 centred at (gu) : 89.16050 90.51135 90.19559 assigned negative charge : -312.0312 centred at (gu) : 89.30124 90.44513 90.27613 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7799 nv = 96 ne = 84 npr = 41617 no. pairs analyzed = 41617 no. exposed pairs = 2585 no. arc points = 17640 no. surface atoms = 881 nbur = 1400 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 606 mr = 4588 m= 6 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5706907E-07 2.0519098E-08 midg,1,midg; midg,igrid,midg 3.0290103E-08 1.6541507E-07 1,midg,midg; igrid,midg,midg 2.5217753E-07 -2.8632790E-08 gauss-seidel spectral radius is 0.9903375 estimated iterations to convergence 83 setup time was (sec) 0.5700000 now iterating at: 06:02:00 rms-change max change #iterations 0.2349722 37.77865 at 10iterations 3.1967744E-02 4.007999 at 20iterations 4.9770162E-03 0.5901794 at 30iterations 1.0424483E-03 0.1296844 at 40iterations 3.1721068E-04 3.3210754E-02 at 50iterations finished qdiffx linear iterations at : 06:02:03 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 3.1721068E-04 3.3210754E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 06:02:04 3.724u 0.193s 0:04.55 85.9% 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 Tue Oct 11 2011 at 06:02:04 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.203970 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): 25.62500 72.11100 ymin,ymax (A): -18.59700 29.86100 zmin,zma (A): 4.167000 46.30400 x,y,z range (A): 46.48600 48.45800 42.13700 scale (grids/A): 2.203970 object centre (A): 48.86800 5.632000 25.23550 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 317.9760 centred at (gu) : 87.48132 91.53412 90.58696 assigned negative charge : -312.0312 centred at (gu) : 87.90401 91.33548 90.82835 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17640 grid for indexing accessible points = 1.400000 m= 35271 mr = 58840 m= 7639 mr = 27286 m= 854 mr = 5330 m= 28 mr = 442 m= 0 mr = 9 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 33947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15557 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) : 0.7346568 object centre at (A) : 48.86800 5.632000 25.23550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4493081E-02 3.1088645E-02 midg,1,midg; midg,igrid,midg 4.7992703E-02 3.4012992E-02 1,midg,midg; igrid,midg,midg 4.9926322E-02 -6.2836327E-02 gauss-seidel spectral radius is 0.9989069 estimated iterations to convergence 239 setup time was (sec) 1.070000 now iterating at: 06:02:06 rms-change max change #iterations 4.945005 220.3159 at 10iterations 2.502726 79.51487 at 20iterations 1.274562 34.55811 at 30iterations 0.6476264 17.89049 at 40iterations 0.3278916 9.276460 at 50iterations 0.1670319 4.877127 at 60iterations 8.5130773E-02 2.334053 at 70iterations 4.3568429E-02 1.197897 at 80iterations 2.2404475E-02 0.7281895 at 90iterations 1.1666081E-02 0.3510361 at 100iterations 6.1246208E-03 0.1669464 at 110iterations 3.3461063E-03 9.7671509E-02 at 120iterations finished qdiffx linear iterations at : 06:02:13 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 3.3461063E-03 9.7671509E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.150000 DelPhi exited at 06:02:14 9.150u 0.280s 0:10.24 92.0% 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 Tue Oct 11 2011 at 06:02:15 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.305956 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): 25.62500 72.11100 ymin,ymax (A): -18.59700 29.86100 zmin,zma (A): 4.167000 46.30400 x,y,z range (A): 46.48600 48.45800 42.13700 scale (grids/A): 3.305956 object centre (A): 48.86800 5.632000 25.23550 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 317.9760 centred at (gu) : 86.22210 92.30108 90.88046 assigned negative charge : -312.0312 centred at (gu) : 86.85595 92.00314 91.24247 start vw surface at 0.1800000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 188863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17640 grid for indexing accessible points = 1.400000 m= 107214 mr = 141181 m= 47078 mr = 90168 m= 14746 mr = 39278 m= 3297 mr = 11775 m= 486 mr = 2428 m= 36 mr = 339 m= 0 mr = 9 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.180000 number of dielectric boundary points 76542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 15640 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) : 2.203970 object centre at (A) : 48.86800 5.632000 25.23550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9447012E-02 0.2598051 midg,1,midg; midg,igrid,midg 0.3271399 0.1689052 1,midg,midg; igrid,midg,midg 0.4822158 -0.7088846 gauss-seidel spectral radius is 0.9993169 estimated iterations to convergence 302 setup time was (sec) 2.530000 now iterating at: 06:02:18 rms-change max change #iterations 10.78220 319.0255 at 10iterations 6.442713 125.2883 at 20iterations 3.834392 75.28592 at 30iterations 2.286146 61.47665 at 40iterations 1.357183 24.01978 at 50iterations 0.8043565 14.13850 at 60iterations 0.4763048 9.196594 at 70iterations 0.2818660 4.823196 at 80iterations 0.1668279 2.827152 at 90iterations 9.8695375E-02 1.727184 at 100iterations 5.8572255E-02 1.013981 at 110iterations 3.4965590E-02 0.5611706 at 120iterations 2.1127172E-02 0.3759918 at 130iterations 1.3022763E-02 0.2274895 at 140iterations 8.3012115E-03 0.1531448 at 150iterations 5.5833203E-03 0.1065712 at 160iterations 3.9807796E-03 7.6911926E-02 at 170iterations 3.0223329E-03 5.0949097E-02 at 180iterations finished qdiffx linear iterations at : 06:02:29 total time elapsed so far: 14.08000 # loops : 180 mean,max change (kT/e) : 3.0223329E-03 5.0949097E-02 energy calculations done at 14.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.26000 DelPhi exited at 06:02:30 14.265u 0.275s 0:15.22 95.4% 0+0k 0+0io 0pf+0w