Sat Oct 8 11:36:21 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 Sat Oct 8 2011 at 11:36:21 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: GLM 295 has a net charge of -0.6000 !!! WARNING: ZN4 472 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6368971 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): -23.36600 32.53000 ymin,ymax (A): -1.801000 51.28900 zmin,zma (A): 12.25600 60.06400 x,y,z range (A): 55.89600 53.09000 47.80800 scale (grids/A): 0.6368971 object centre (A): 4.582000 24.74400 36.16000 number of atom coordinates read : 3363 total number of charged atoms : 3216 net assigned charge : -1.599976 assigned positive charge : 510.7845 centred at (gu) : 90.71770 90.70538 89.15140 assigned negative charge : -512.3856 centred at (gu) : 90.78224 90.50977 89.30186 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8930 nv = 96 ne = 84 npr = 71575 no. pairs analyzed = 71575 no. exposed pairs = 3619 no. arc points = 24629 no. surface atoms = 1250 nbur = 2113 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 5487 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.3500000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2408 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2320643E-08 -1.9997289E-08 midg,1,midg; midg,igrid,midg -2.6306848E-08 2.8794574E-08 1,midg,midg; igrid,midg,midg 5.6565690E-09 -1.3580236E-08 gauss-seidel spectral radius is 0.9872797 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 11:36:22 rms-change max change #iterations 0.1675444 21.76450 at 10iterations 1.6816169E-02 2.100666 at 20iterations 1.6643294E-03 0.2035046 at 30iterations 1.6504504E-04 1.8680573E-02 at 40iterations 1.6453463E-05 2.2678375E-03 at 50iterations finished qdiffx linear iterations at : 11:36:24 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.6453463E-05 2.2678375E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 11:36:26 3.351u 0.195s 0:04.75 74.5% 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 Sat Oct 8 2011 at 11:36:26 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: GLM 295 has a net charge of -0.6000 !!! WARNING: ZN4 472 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.910691 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): -23.36600 32.53000 ymin,ymax (A): -1.801000 51.28900 zmin,zma (A): 12.25600 60.06400 x,y,z range (A): 55.89600 53.09000 47.80800 scale (grids/A): 1.910691 object centre (A): 4.582000 24.74400 36.16000 number of atom coordinates read : 3363 total number of charged atoms : 3216 net assigned charge : -1.599976 assigned positive charge : 510.7845 centred at (gu) : 92.15216 92.11509 87.45307 assigned negative charge : -512.3856 centred at (gu) : 92.34603 91.52894 87.90509 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 96639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24629 grid for indexing accessible points = 1.400000 m= 37033 mr = 71332 m= 5914 mr = 29248 m= 339 mr = 4020 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2930 time to turn everything in is 0.6600000 number of dielectric boundary points 35208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 25297 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) : 0.6368971 object centre at (A) : 4.582000 24.74400 36.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0158367E-03 -5.4343864E-02 midg,1,midg; midg,igrid,midg -3.6398180E-02 3.6421876E-02 1,midg,midg; igrid,midg,midg 4.8614590E-04 -1.2544212E-02 gauss-seidel spectral radius is 0.9986967 estimated iterations to convergence 219 setup time was (sec) 0.9400000 now iterating at: 11:36:27 rms-change max change #iterations 4.984923 172.9893 at 10iterations 2.370892 69.70344 at 20iterations 1.129726 31.38387 at 30iterations 0.5375795 14.53502 at 40iterations 0.2574329 7.274773 at 50iterations 0.1230746 3.373033 at 60iterations 5.8798097E-02 1.567390 at 70iterations 2.8121768E-02 0.8263097 at 80iterations 1.3421535E-02 0.3802872 at 90iterations 6.4070635E-03 0.1929455 at 100iterations 3.0666785E-03 8.2565308E-02 at 110iterations 1.4652609E-03 4.1643143E-02 at 120iterations finished qdiffx linear iterations at : 11:36:33 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.4652609E-03 4.1643143E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 11:36:34 7.736u 0.232s 0:08.56 92.9% 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 Sat Oct 8 2011 at 11:36:34 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: GLM 295 has a net charge of -0.6000 !!! WARNING: ZN4 472 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.866037 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): -23.36600 32.53000 ymin,ymax (A): -1.801000 51.28900 zmin,zma (A): 12.25600 60.06400 x,y,z range (A): 55.89600 53.09000 47.80800 scale (grids/A): 2.866037 object centre (A): 4.582000 24.74400 36.16000 number of atom coordinates read : 3363 total number of charged atoms : 3216 net assigned charge : -1.599976 assigned positive charge : 510.7845 centred at (gu) : 93.22794 93.17243 86.17926 assigned negative charge : -512.3856 centred at (gu) : 93.51883 92.29325 86.85740 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 223408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24629 grid for indexing accessible points = 1.400000 m= 119462 mr = 171496 m= 45198 mr = 101793 m= 10821 mr = 38284 m= 1430 mr = 8492 m= 87 mr = 955 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 10283 time to turn everything in is 1.720000 number of dielectric boundary points 79359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 25726 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) : 1.910691 object centre at (A) : 4.582000 24.74400 36.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0784626E-02 -0.6395519 midg,1,midg; midg,igrid,midg -0.3636021 0.3405796 1,midg,midg; igrid,midg,midg -0.1630211 -0.1242175 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 2.020000 now iterating at: 11:36:37 rms-change max change #iterations 11.49541 318.8221 at 10iterations 6.744622 126.8492 at 20iterations 3.942121 94.96893 at 30iterations 2.294746 49.53212 at 40iterations 1.334720 25.93533 at 50iterations 0.7783431 12.52744 at 60iterations 0.4510940 6.897591 at 70iterations 0.2618551 4.363223 at 80iterations 0.1518011 2.472235 at 90iterations 8.7863274E-02 1.306072 at 100iterations 5.0993957E-02 0.7900505 at 110iterations 2.9544471E-02 0.5208092 at 120iterations 1.7087724E-02 0.2735500 at 130iterations 9.9017741E-03 0.1516924 at 140iterations 5.7321116E-03 9.2010498E-02 at 150iterations 3.3181473E-03 5.1074982E-02 at 160iterations 1.9234924E-03 3.1066895E-02 at 170iterations 1.1130712E-03 1.8773437E-02 at 180iterations finished qdiffx linear iterations at : 11:36:47 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 1.1130712E-03 1.8773437E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 11:36:48 12.811u 0.249s 0:13.50 96.6% 0+0k 0+0io 0pf+0w