Sun Oct 9 11:57:52 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+sph.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 = amb.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 Sun Oct 9 2011 at 11:57:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6650973 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): 51.46900 103.8250 ymin,ymax (A): 6.519000 55.58700 zmin,zma (A): 34.53400 88.06000 x,y,z range (A): 52.35601 49.06800 53.52600 scale (grids/A): 0.6650973 object centre (A): 77.64700 31.05300 61.29700 number of atom coordinates read : 2680 total number of charged atoms : 2539 net assigned charge : 0.5000091 assigned positive charge : 382.4843 centred at (gu) : 89.30280 89.50895 92.64678 assigned negative charge : -381.9858 centred at (gu) : 89.47144 89.59057 92.55459 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8548 nv = 96 ne = 84 npr = 52942 no. pairs analyzed = 52942 no. exposed pairs = 3638 no. arc points = 26182 no. surface atoms = 1232 nbur = 1448 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 592 mr = 4510 m= 0 mr = 112 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2317 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9582 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1506961E-08 3.6234098E-08 midg,1,midg; midg,igrid,midg 2.0300449E-08 -1.5874360E-08 1,midg,midg; igrid,midg,midg 4.2812747E-08 -3.2176519E-08 gauss-seidel spectral radius is 0.9883112 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 11:57:53 rms-change max change #iterations 0.1710753 25.03611 at 10iterations 1.8670781E-02 2.487183 at 20iterations 2.1411616E-03 0.2868118 at 30iterations 3.6204074E-04 5.9076309E-02 at 40iterations 1.0125782E-04 1.9100189E-02 at 50iterations finished qdiffx linear iterations at : 11:57:56 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.0125782E-04 1.9100189E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:57:56 3.382u 0.165s 0:03.86 91.7% 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 Sun Oct 9 2011 at 11:57:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.995292 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): 51.46900 103.8250 ymin,ymax (A): 6.519000 55.58700 zmin,zma (A): 34.53400 88.06000 x,y,z range (A): 52.35601 49.06800 53.52600 scale (grids/A): 1.995292 object centre (A): 77.64700 31.05300 61.29700 number of atom coordinates read : 2680 total number of charged atoms : 2539 net assigned charge : 0.5000091 assigned positive charge : 382.4843 centred at (gu) : 87.90755 88.52596 97.93970 assigned negative charge : -381.9858 centred at (gu) : 88.41434 88.77135 97.66368 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26182 grid for indexing accessible points = 1.400000 m= 34899 mr = 60508 m= 7398 mr = 25353 m= 628 mr = 4956 m= 4 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.6700000 number of dielectric boundary points 41737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20106 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) : 0.6650973 object centre at (A) : 77.64700 31.05300 61.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4332286E-02 8.1302345E-02 midg,1,midg; midg,igrid,midg 2.2423169E-02 -1.1288960E-02 1,midg,midg; igrid,midg,midg 2.9362548E-02 -4.5493077E-02 gauss-seidel spectral radius is 0.9987891 estimated iterations to convergence 228 setup time was (sec) 0.9600000 now iterating at: 11:57:57 rms-change max change #iterations 4.648471 192.5795 at 10iterations 2.285012 78.16775 at 20iterations 1.118464 31.79574 at 30iterations 0.5475796 16.41721 at 40iterations 0.2688962 7.870663 at 50iterations 0.1318669 3.777287 at 60iterations 6.4642712E-02 1.799831 at 70iterations 3.1669293E-02 0.9572333 at 80iterations 1.5541321E-02 0.4269292 at 90iterations 7.6174322E-03 0.2153873 at 100iterations 3.7581085E-03 0.1284161 at 110iterations 1.8613967E-03 5.0170898E-02 at 120iterations finished qdiffx linear iterations at : 11:58:04 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.8613967E-03 5.0170898E-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) 7.800000 DelPhi exited at 11:58:05 7.805u 0.160s 0:08.32 95.6% 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 Sun Oct 9 2011 at 11:58:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.992938 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): 51.46900 103.8250 ymin,ymax (A): 6.519000 55.58700 zmin,zma (A): 34.53400 88.06000 x,y,z range (A): 52.35601 49.06800 53.52600 scale (grids/A): 2.992938 object centre (A): 77.64700 31.05300 61.29700 number of atom coordinates read : 2680 total number of charged atoms : 2539 net assigned charge : 0.5000091 assigned positive charge : 382.4843 centred at (gu) : 86.86107 87.78873 101.9093 assigned negative charge : -381.9858 centred at (gu) : 87.62156 88.15684 101.4956 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 207266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26182 grid for indexing accessible points = 1.400000 m= 107242 mr = 146852 m= 45363 mr = 86494 m= 13958 mr = 36401 m= 2846 mr = 10789 m= 234 mr = 2126 m= 5 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 1.740000 number of dielectric boundary points 94119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 20312 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) : 1.995292 object centre at (A) : 77.64700 31.05300 61.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1297004 1.018865 midg,1,midg; midg,igrid,midg 0.2335479 -0.3169515 1,midg,midg; igrid,midg,midg 0.2173869 -0.4170884 gauss-seidel spectral radius is 0.9993250 estimated iterations to convergence 304 setup time was (sec) 2.060000 now iterating at: 11:58:07 rms-change max change #iterations 10.81613 488.0546 at 10iterations 6.564610 159.1479 at 20iterations 3.956096 94.45445 at 30iterations 2.377802 54.69508 at 40iterations 1.423193 28.99851 at 50iterations 0.8476174 16.01138 at 60iterations 0.5051832 9.756189 at 70iterations 0.2999676 5.357634 at 80iterations 0.1777711 3.264252 at 90iterations 0.1053599 1.800749 at 100iterations 6.2309388E-02 1.131805 at 110iterations 3.6880102E-02 0.6735673 at 120iterations 2.1823017E-02 0.3636303 at 130iterations 1.2875403E-02 0.2136383 at 140iterations 7.6310029E-03 0.1301250 at 150iterations 4.5277798E-03 7.5130463E-02 at 160iterations 2.6793198E-03 4.2800903E-02 at 170iterations 1.6050535E-03 2.7868271E-02 at 180iterations finished qdiffx linear iterations at : 11:58:18 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.6050535E-03 2.7868271E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 11:58:18 12.943u 0.177s 0:13.40 97.8% 0+0k 0+0io 0pf+0w