Tue Oct 11 07:51:18 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 07:51:18 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 !!! WARNING: HIQ 59 has a net charge of 0.5140 !!! WARNING: GLM 208 has a net charge of -0.0940 !!! WARNING: SEP 211 has a net charge of -0.4750 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: 0.6386796 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): -13.59500 42.14500 ymin,ymax (A): -22.55300 25.34800 zmin,zma (A): -5.768000 40.32600 x,y,z range (A): 55.74000 47.90100 46.09400 scale (grids/A): 0.6386796 object centre (A): 14.27500 1.397500 17.27900 number of atom coordinates read : 2759 total number of charged atoms : 2389 net assigned charge : 7.945013 assigned positive charge : 386.5190 centred at (gu) : 90.18625 88.94502 89.06628 assigned negative charge : -378.5747 centred at (gu) : 90.20053 88.93451 89.23952 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6748 nv = 96 ne = 84 npr = 51697 no. pairs analyzed = 51697 no. exposed pairs = 3004 no. arc points = 20485 no. surface atoms = 1035 nbur = 1724 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3822 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2000000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2048 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6174320E-08 -6.7554913E-09 midg,1,midg; midg,igrid,midg 1.2182214E-08 9.7319415E-09 1,midg,midg; igrid,midg,midg 1.2038052E-08 9.7476462E-09 gauss-seidel spectral radius is 0.9872851 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 07:51:19 rms-change max change #iterations 0.1443294 21.25458 at 10iterations 1.4909096E-02 2.182413 at 20iterations 1.9023895E-03 0.2890091 at 30iterations 3.7073309E-04 5.2932739E-02 at 40iterations 9.1878392E-05 1.3666153E-02 at 50iterations finished qdiffx linear iterations at : 07:51:22 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 9.1878392E-05 1.3666153E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:51:22 3.323u 0.185s 0:03.88 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 Tue Oct 11 2011 at 07:51:22 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 !!! WARNING: HIQ 59 has a net charge of 0.5140 !!! WARNING: GLM 208 has a net charge of -0.0940 !!! WARNING: SEP 211 has a net charge of -0.4750 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: 1.916039 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): -13.59500 42.14500 ymin,ymax (A): -22.55300 25.34800 zmin,zma (A): -5.768000 40.32600 x,y,z range (A): 55.74000 47.90100 46.09400 scale (grids/A): 1.916039 object centre (A): 14.27500 1.397500 17.27900 number of atom coordinates read : 2759 total number of charged atoms : 2389 net assigned charge : 7.945013 assigned positive charge : 386.5190 centred at (gu) : 90.55844 86.83470 87.19831 assigned negative charge : -378.5747 centred at (gu) : 90.60141 86.80334 87.71841 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20485 grid for indexing accessible points = 1.400000 m= 26831 mr = 51637 m= 3937 mr = 20014 m= 206 mr = 2326 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18781 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) : 0.6386796 object centre at (A) : 14.27500 1.397500 17.27900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7166269E-02 -7.1333814E-03 midg,1,midg; midg,igrid,midg 9.7953137E-03 1.8515322E-02 1,midg,midg; igrid,midg,midg 2.1196393E-02 2.7419813E-02 gauss-seidel spectral radius is 0.9986352 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 07:51:23 rms-change max change #iterations 4.247015 178.6256 at 10iterations 2.004433 69.11247 at 20iterations 0.9354697 29.57084 at 30iterations 0.4422677 15.56668 at 40iterations 0.2072297 6.668928 at 50iterations 9.7370788E-02 2.980638 at 60iterations 4.5947786E-02 1.417052 at 70iterations 2.1665692E-02 0.7228718 at 80iterations 1.0273173E-02 0.3041201 at 90iterations 4.9230228E-03 0.1548907 at 100iterations 2.3822503E-03 8.2401276E-02 at 110iterations 1.1807155E-03 3.6643982E-02 at 120iterations finished qdiffx linear iterations at : 07:51:30 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 1.1807155E-03 3.6643982E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 07:51:31 7.653u 0.190s 0:08.96 87.5% 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 07:51:31 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 !!! WARNING: HIQ 59 has a net charge of 0.5140 !!! WARNING: GLM 208 has a net charge of -0.0940 !!! WARNING: SEP 211 has a net charge of -0.4750 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: 2.874058 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): -13.59500 42.14500 ymin,ymax (A): -22.55300 25.34800 zmin,zma (A): -5.768000 40.32600 x,y,z range (A): 55.74000 47.90100 46.09400 scale (grids/A): 2.874058 object centre (A): 14.27500 1.397500 17.27900 number of atom coordinates read : 2759 total number of charged atoms : 2389 net assigned charge : 7.945013 assigned positive charge : 386.5190 centred at (gu) : 90.83748 85.25182 85.79747 assigned negative charge : -378.5747 centred at (gu) : 90.90211 85.20498 86.57760 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20485 grid for indexing accessible points = 1.400000 m= 87030 mr = 124723 m= 30810 mr = 72138 m= 6922 mr = 24770 m= 962 mr = 5013 m= 52 mr = 620 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 67304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19104 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) : 1.916039 object centre at (A) : 14.27500 1.397500 17.27900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4325298 -0.1381176 midg,1,midg; midg,igrid,midg 7.2177991E-02 0.2012114 1,midg,midg; igrid,midg,midg 9.9906191E-02 0.2123059 gauss-seidel spectral radius is 0.9992479 estimated iterations to convergence 288 setup time was (sec) 1.170000 now iterating at: 07:51:33 rms-change max change #iterations 9.863440 349.8719 at 10iterations 5.725216 144.5784 at 20iterations 3.303928 81.76301 at 30iterations 1.909259 38.41993 at 40iterations 1.098860 19.83245 at 50iterations 0.6315999 11.50090 at 60iterations 0.3620055 6.398157 at 70iterations 0.2079335 4.049416 at 80iterations 0.1191368 2.169447 at 90iterations 6.8331257E-02 1.356335 at 100iterations 3.9148286E-02 0.7186584 at 110iterations 2.2426482E-02 0.4676514 at 120iterations 1.2953926E-02 0.2506857 at 130iterations 7.4652759E-03 0.1310349 at 140iterations 4.3544527E-03 7.7697754E-02 at 150iterations 2.5770573E-03 4.7363281E-02 at 160iterations 1.5659264E-03 3.0323029E-02 at 170iterations 9.8247023E-04 2.0767212E-02 at 180iterations finished qdiffx linear iterations at : 07:51:44 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 9.8247023E-04 2.0767212E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 07:51:45 12.300u 0.208s 0:13.11 95.3% 0+0k 0+0io 0pf+0w