Sat Oct 15 13:05:12 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 Sat Oct 15 2011 at 13:05:12 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2474 !!! WARNING: GLM 438 has a net charge of -0.0940 !!! WARNING: SEP 568 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6295760 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 0.6295760 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2330 net assigned charge : 7.931008 assigned positive charge : 369.3830 centred at (gu) : 90.75855 90.25351 90.49072 assigned negative charge : -361.4527 centred at (gu) : 90.90066 90.39325 90.29390 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6527 nv = 96 ne = 84 npr = 49925 no. pairs analyzed = 49925 no. exposed pairs = 3112 no. arc points = 21900 no. surface atoms = 1061 nbur = 1413 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3429 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2231 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7947 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9311810E-09 2.6998398E-08 midg,1,midg; midg,igrid,midg 1.8731544E-08 -3.1540421E-09 1,midg,midg; igrid,midg,midg 1.6961952E-08 -3.8271191E-09 gauss-seidel spectral radius is 0.9869216 estimated iterations to convergence 72 setup time was (sec) 0.6400000 now iterating at: 13:05:13 rms-change max change #iterations 0.1295497 19.15220 at 10iterations 1.2156151E-02 1.806740 at 20iterations 1.1561548E-03 0.1708918 at 30iterations 1.1143205E-04 1.5768051E-02 at 40iterations 1.0757783E-05 1.6250610E-03 at 50iterations finished qdiffx linear iterations at : 13:05:18 total time elapsed so far: 5.040000 # loops : 50 mean,max change (kT/e) : 1.0757783E-05 1.6250610E-03 energy calculations done at 5.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 13:05:18 5.208u 0.487s 0:06.06 93.7% 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 Sat Oct 15 2011 at 13:05:18 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2474 !!! WARNING: GLM 438 has a net charge of -0.0940 !!! WARNING: SEP 568 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.888728 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 1.888728 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2330 net assigned charge : 7.931008 assigned positive charge : 369.3830 centred at (gu) : 92.27504 90.75977 91.47176 assigned negative charge : -361.4527 centred at (gu) : 92.70195 91.17963 90.88145 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 23746 mr = 48210 m= 3306 mr = 16571 m= 205 mr = 1828 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 676 time to turn everything in is 0.7200000 number of dielectric boundary points 31373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 18288 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) : 0.6295760 object centre at (A) : 7.092002 2.418000 14.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1622675E-04 4.0592700E-02 midg,1,midg; midg,igrid,midg 2.2944354E-02 -3.8795486E-02 1,midg,midg; igrid,midg,midg 2.9861374E-02 4.8838747E-03 gauss-seidel spectral radius is 0.9985948 estimated iterations to convergence 211 setup time was (sec) 1.090000 now iterating at: 13:05:20 rms-change max change #iterations 4.009069 165.1099 at 10iterations 1.850610 64.30815 at 20iterations 0.8611028 31.22300 at 30iterations 0.3973730 14.51212 at 40iterations 0.1842825 7.154674 at 50iterations 8.5213572E-02 2.945240 at 60iterations 3.9480671E-02 1.260425 at 70iterations 1.8306404E-02 0.5927610 at 80iterations 8.4670242E-03 0.2686384 at 90iterations 3.9176731E-03 0.1240988 at 100iterations 1.8236063E-03 5.5514336E-02 at 110iterations 8.4395154E-04 2.9167175E-02 at 120iterations finished qdiffx linear iterations at : 13:05:31 total time elapsed so far: 12.62000 # loops : 120 mean,max change (kT/e) : 8.4395154E-04 2.9167175E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 13:05:32 12.788u 0.532s 0:13.74 96.8% 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 Sat Oct 15 2011 at 13:05:32 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2474 !!! WARNING: GLM 438 has a net charge of -0.0940 !!! WARNING: SEP 568 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.833092 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 2.833092 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2330 net assigned charge : 7.931008 assigned positive charge : 369.3830 centred at (gu) : 93.41248 91.13951 92.20753 assigned negative charge : -361.4527 centred at (gu) : 94.05275 91.76931 91.32213 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 163839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 79007 mr = 117500 m= 25863 mr = 63103 m= 5882 mr = 19627 m= 842 mr = 4055 m= 44 mr = 515 m= 0 mr = 13 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2155 time to turn everything in is 1.600000 number of dielectric boundary points 70664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 18640 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) : 1.888728 object centre at (A) : 7.092002 2.418000 14.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7006162E-02 0.4568815 midg,1,midg; midg,igrid,midg 0.3219248 -0.5343891 1,midg,midg; igrid,midg,midg 0.3959895 5.4232426E-02 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 2.030000 now iterating at: 13:05:35 rms-change max change #iterations 9.587887 340.9509 at 10iterations 5.622264 127.7186 at 20iterations 3.253038 70.67001 at 30iterations 1.887744 38.47344 at 40iterations 1.087256 21.45474 at 50iterations 0.6263860 11.72218 at 60iterations 0.3607767 7.321831 at 70iterations 0.2066777 4.068958 at 80iterations 0.1187165 2.498557 at 90iterations 6.8148628E-02 1.375517 at 100iterations 3.9073333E-02 0.7160110 at 110iterations 2.2408247E-02 0.4154816 at 120iterations 1.2836684E-02 0.2579855 at 130iterations 7.3329229E-03 0.1405632 at 140iterations 4.2029414E-03 7.8116417E-02 at 150iterations 2.4109161E-03 4.6239853E-02 at 160iterations 1.3766419E-03 2.4544358E-02 at 170iterations 7.8830507E-04 1.4156342E-02 at 180iterations finished qdiffx linear iterations at : 13:05:54 total time elapsed so far: 21.09000 # loops : 180 mean,max change (kT/e) : 7.8830507E-04 1.4156342E-02 energy calculations done at 21.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.28000 DelPhi exited at 13:05:54 21.284u 0.530s 0:22.11 98.6% 0+0k 0+0io 0pf+0w