Tue Oct 11 05:17:55 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 Tue Oct 11 2011 at 05:17:55 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG5 577 has a net charge of 1.4000 !!! WARNING: ZN5 578 has a net charge of 1.4000 !!! WARNING: ZN5 579 has a net charge of 1.4000 !!! WARNING: ZN5 580 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: 0.6895349 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): 15.65800 62.97800 ymin,ymax (A): -3.554000 33.68100 zmin,zma (A): 20.16900 71.79800 x,y,z range (A): 47.32000 37.23500 51.62901 scale (grids/A): 0.6895349 object centre (A): 39.31800 15.06350 45.98350 number of atom coordinates read : 2306 total number of charged atoms : 1984 net assigned charge : 11.80001 assigned positive charge : 326.7839 centred at (gu) : 91.47495 89.76231 89.21096 assigned negative charge : -314.9841 centred at (gu) : 91.55357 89.70564 89.09264 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6774 nv = 96 ne = 84 npr = 42618 no. pairs analyzed = 42618 no. exposed pairs = 2514 no. arc points = 17392 no. surface atoms = 860 nbur = 1446 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3922 m= 1 mr = 81 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 0.2700000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1707 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7709 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9438089E-08 8.8947310E-08 midg,1,midg; midg,igrid,midg 4.8494051E-08 8.0023995E-08 1,midg,midg; igrid,midg,midg 6.8314264E-08 5.1355272E-08 gauss-seidel spectral radius is 0.9890431 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 05:17:56 rms-change max change #iterations 0.1891961 26.89090 at 10iterations 2.2124309E-02 2.970966 at 20iterations 2.5626933E-03 0.3413315 at 30iterations 3.3365996E-04 5.6110382E-02 at 40iterations 5.0910854E-05 6.6070557E-03 at 50iterations finished qdiffx linear iterations at : 05:17:58 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 5.0910854E-05 6.6070557E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 05:17:59 3.052u 0.123s 0:03.61 87.8% 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 Tue Oct 11 2011 at 05:17:59 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG5 577 has a net charge of 1.4000 !!! WARNING: ZN5 578 has a net charge of 1.4000 !!! WARNING: ZN5 579 has a net charge of 1.4000 !!! WARNING: ZN5 580 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: 2.068605 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): 15.65800 62.97800 ymin,ymax (A): -3.554000 33.68100 zmin,zma (A): 20.16900 71.79800 x,y,z range (A): 47.32000 37.23500 51.62901 scale (grids/A): 2.068605 object centre (A): 39.31800 15.06350 45.98350 number of atom coordinates read : 2306 total number of charged atoms : 1984 net assigned charge : 11.80001 assigned positive charge : 326.7839 centred at (gu) : 94.42476 89.28676 87.63270 assigned negative charge : -314.9841 centred at (gu) : 94.66085 89.11707 87.27791 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17392 grid for indexing accessible points = 1.400000 m= 28745 mr = 51642 m= 5364 mr = 22026 m= 435 mr = 3602 m= 5 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15746 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) : 0.6895349 object centre at (A) : 39.31800 15.06350 45.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9302764E-02 6.1737541E-02 midg,1,midg; midg,igrid,midg 3.2181900E-02 4.7459166E-02 1,midg,midg; igrid,midg,midg 2.7238639E-02 3.9438449E-02 gauss-seidel spectral radius is 0.9987768 estimated iterations to convergence 226 setup time was (sec) 0.7900000 now iterating at: 05:18:00 rms-change max change #iterations 4.460352 223.3245 at 10iterations 2.186586 77.99203 at 20iterations 1.060637 31.80107 at 30iterations 0.5184501 16.94176 at 40iterations 0.2523783 8.261497 at 50iterations 0.1237543 3.943268 at 60iterations 6.0372483E-02 1.894318 at 70iterations 2.9536771E-02 1.080487 at 80iterations 1.4422759E-02 0.5087023 at 90iterations 7.0427796E-03 0.1979752 at 100iterations 3.4502079E-03 0.1111999 at 110iterations 1.6918444E-03 5.0689697E-02 at 120iterations finished qdiffx linear iterations at : 05:18:06 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 1.6918444E-03 5.0689697E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 05:18:07 6.802u 0.156s 0:07.51 92.5% 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 05:18:07 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2306 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG5 577 has a net charge of 1.4000 !!! WARNING: ZN5 578 has a net charge of 1.4000 !!! WARNING: ZN5 579 has a net charge of 1.4000 !!! WARNING: ZN5 580 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.102907 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): 15.65800 62.97800 ymin,ymax (A): -3.554000 33.68100 zmin,zma (A): 20.16900 71.79800 x,y,z range (A): 47.32000 37.23500 51.62901 scale (grids/A): 3.102907 object centre (A): 39.31800 15.06350 45.98350 number of atom coordinates read : 2306 total number of charged atoms : 1984 net assigned charge : 11.80001 assigned positive charge : 326.7839 centred at (gu) : 96.63717 88.93015 86.44901 assigned negative charge : -314.9841 centred at (gu) : 96.99129 88.67566 85.91686 start vw surface at 0.1500000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 166840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17392 grid for indexing accessible points = 1.400000 m= 90622 mr = 124648 m= 35517 mr = 75616 m= 10068 mr = 29274 m= 1918 mr = 7891 m= 181 mr = 1428 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.610000 number of dielectric boundary points 66177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 15872 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) : 2.068605 object centre at (A) : 39.31800 15.06350 45.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5046809 0.4940875 midg,1,midg; midg,igrid,midg 0.2967129 0.4208006 1,midg,midg; igrid,midg,midg 0.2270844 0.6260986 gauss-seidel spectral radius is 0.9992821 estimated iterations to convergence 295 setup time was (sec) 1.880000 now iterating at: 05:18:09 rms-change max change #iterations 10.07382 393.2296 at 10iterations 5.929312 140.7926 at 20iterations 3.489446 68.83439 at 30iterations 2.041685 41.80176 at 40iterations 1.195155 27.49328 at 50iterations 0.7008815 12.66014 at 60iterations 0.4080777 8.331940 at 70iterations 0.2377666 4.376057 at 80iterations 0.1391598 2.632465 at 90iterations 8.0734007E-02 1.564964 at 100iterations 4.6975054E-02 0.9262524 at 110iterations 2.7312553E-02 0.4800549 at 120iterations 1.5905747E-02 0.2872772 at 130iterations 9.2432536E-03 0.1760063 at 140iterations 5.3703212E-03 9.2100143E-02 at 150iterations 3.1274571E-03 5.5866241E-02 at 160iterations 1.8180851E-03 3.2469749E-02 at 170iterations 1.0604862E-03 1.9717216E-02 at 180iterations finished qdiffx linear iterations at : 05:18:18 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 1.0604862E-03 1.9717216E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 05:18:18 11.247u 0.172s 0:11.75 97.1% 0+0k 0+0io 0pf+0w