Mon Jan 23 21:01:35 PST 2012 #!/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 Mon Jan 23 2012 at 21:01:37 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: HIZ 190 has a net charge of 0.2000 !!! WARNING: HIZ 194 has a net charge of 0.2000 !!! WARNING: HIZ 200 has a net charge of 0.2000 !!! WARNING: ZN1 901 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6092030 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): 10.32100 68.75800 ymin,ymax (A): 1.207000 50.38300 zmin,zma (A): -14.55000 35.81500 x,y,z range (A): 58.43700 49.17600 50.36500 scale (grids/A): 0.6092030 object centre (A): 39.53950 25.79500 10.63250 number of atom coordinates read : 2498 total number of charged atoms : 2358 net assigned charge : -3.999985 assigned positive charge : 382.3412 centred at (gu) : 90.00533 91.02808 90.59098 assigned negative charge : -386.3415 centred at (gu) : 90.10601 90.99424 90.49160 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5939 nv = 96 ne = 84 npr = 51704 no. pairs analyzed = 51704 no. exposed pairs = 2909 no. arc points = 20675 no. surface atoms = 993 nbur = 1505 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3265 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2300000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2078 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2875296E-09 2.7415710E-09 midg,1,midg; midg,igrid,midg -3.1721605E-09 -8.8175423E-10 1,midg,midg; igrid,midg,midg 2.4370115E-09 -7.2488762E-09 gauss-seidel spectral radius is 0.9860365 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 21:01:37 rms-change max change #iterations 0.1142771 17.80528 at 10iterations 1.0120261E-02 1.473864 at 20iterations 8.8661601E-04 0.1199431 at 30iterations 8.0634585E-05 1.3263702E-02 at 40iterations 7.0850379E-06 1.1482239E-03 at 50iterations finished qdiffx linear iterations at : 21:01:40 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 7.0850379E-06 1.1482239E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 21:01:41 3.512u 0.196s 0:05.76 64.2% 0+0k 0+45736io 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 Mon Jan 23 2012 at 21:01:42 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: HIZ 190 has a net charge of 0.2000 !!! WARNING: HIZ 194 has a net charge of 0.2000 !!! WARNING: HIZ 200 has a net charge of 0.2000 !!! WARNING: ZN1 901 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.827609 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): 10.32100 68.75800 ymin,ymax (A): 1.207000 50.38300 zmin,zma (A): -14.55000 35.81500 x,y,z range (A): 58.43700 49.17600 50.36500 scale (grids/A): 1.827609 object centre (A): 39.53950 25.79500 10.63250 number of atom coordinates read : 2498 total number of charged atoms : 2358 net assigned charge : -3.999985 assigned positive charge : 382.3412 centred at (gu) : 90.01556 93.08376 91.77246 assigned negative charge : -386.3415 centred at (gu) : 90.31783 92.98269 91.47452 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 65441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20675 grid for indexing accessible points = 1.400000 m= 21991 mr = 45539 m= 3259 mr = 16053 m= 182 mr = 2074 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.4200000 number of dielectric boundary points 27132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18434 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) : 0.6092030 object centre at (A) : 39.53950 25.79500 10.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0525170E-02 8.6474707E-03 midg,1,midg; midg,igrid,midg -7.0320391E-03 1.4348519E-02 1,midg,midg; igrid,midg,midg -1.8369719E-02 -4.5913756E-02 gauss-seidel spectral radius is 0.9985014 estimated iterations to convergence 205 setup time was (sec) 0.6200000 now iterating at: 21:01:44 rms-change max change #iterations 3.920213 174.3234 at 10iterations 1.766203 77.56505 at 20iterations 0.7971105 26.64927 at 30iterations 0.3606946 12.65030 at 40iterations 0.1629388 5.400816 at 50iterations 7.3901802E-02 2.463482 at 60iterations 3.3307053E-02 1.128289 at 70iterations 1.5021581E-02 0.5473983 at 80iterations 6.7952750E-03 0.2492714 at 90iterations 3.0746111E-03 0.1173890 at 100iterations 1.3871909E-03 4.3773711E-02 at 110iterations 6.2777736E-04 2.0584106E-02 at 120iterations finished qdiffx linear iterations at : 21:01:51 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 6.2777736E-04 2.0584106E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 21:01:52 7.941u 0.207s 0:09.45 86.1% 0+0k 0+45232io 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 Mon Jan 23 2012 at 21:01:52 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 ! Automatically converted by prot2crg.py # of charge parameter records: 942 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 !!! WARNING: HIZ 190 has a net charge of 0.2000 !!! WARNING: HIZ 194 has a net charge of 0.2000 !!! WARNING: HIZ 200 has a net charge of 0.2000 !!! WARNING: ZN1 901 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.741414 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): 10.32100 68.75800 ymin,ymax (A): 1.207000 50.38300 zmin,zma (A): -14.55000 35.81500 x,y,z range (A): 58.43700 49.17600 50.36500 scale (grids/A): 2.741414 object centre (A): 39.53950 25.79500 10.63250 number of atom coordinates read : 2498 total number of charged atoms : 2358 net assigned charge : -3.999985 assigned positive charge : 382.3412 centred at (gu) : 90.02313 94.62563 92.65857 assigned negative charge : -386.3415 centred at (gu) : 90.47671 94.47393 92.21170 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 151585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20675 grid for indexing accessible points = 1.400000 m= 73292 mr = 110541 m= 24488 mr = 59786 m= 5878 mr = 19629 m= 857 mr = 4477 m= 44 mr = 596 m= 0 mr = 10 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 1.050000 number of dielectric boundary points 61105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 18863 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) : 1.827609 object centre at (A) : 39.53950 25.79500 10.63250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6850887E-02 0.1583102 midg,1,midg; midg,igrid,midg -9.8032437E-02 0.1957536 1,midg,midg; igrid,midg,midg -0.5614113 -0.5877858 gauss-seidel spectral radius is 0.9992135 estimated iterations to convergence 282 setup time was (sec) 1.280000 now iterating at: 21:01:55 rms-change max change #iterations 9.223087 305.7867 at 10iterations 5.266844 116.6481 at 20iterations 2.979600 64.31802 at 30iterations 1.689312 33.96895 at 40iterations 0.9553142 21.50618 at 50iterations 0.5381650 11.84870 at 60iterations 0.3034689 6.147614 at 70iterations 0.1713039 3.287998 at 80iterations 9.6781537E-02 1.776260 at 90iterations 5.4571245E-02 0.9537516 at 100iterations 3.0803407E-02 0.6393285 at 110iterations 1.7356178E-02 0.3665199 at 120iterations 9.7838184E-03 0.1897631 at 130iterations 5.5254344E-03 0.1052999 at 140iterations 3.1208494E-03 6.6288948E-02 at 150iterations 1.7609114E-03 3.5578251E-02 at 160iterations 9.9176762E-04 1.9241333E-02 at 170iterations 5.6146499E-04 1.0375977E-02 at 180iterations finished qdiffx linear iterations at : 21:02:06 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 5.6146499E-04 1.0375977E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 21:02:07 12.630u 0.224s 0:14.76 87.0% 0+0k 0+45224io 0pf+0w