I am having some difficulty with the mergedx program. I am trying to merge solvent accessibility maps generated in APBS through the 'write smol dx' command. Basically I have calculated the potential and then I want to calculate the accessibility of a hardcore sphere that is of a different radius than water. I modify the original .in files created with inputgen.py (that I ran and then successfully merged with mergedx) to contain a different srad value (i.e 'srad 3.50'), and then write the accessibility grid to .dx file.

The error message I get is:

>$ /usr/local/apbs-0.5.0/tools/mesh/mergedx -v -o 1PV4_003_acc.dx 193 225 225 1PV4_003_acc-PE*
# main:   Reading Headers...
# main:    Reading header from 1PV4_003_acc-PE0.dx...
# main:    Reading header from 1PV4_003_acc-PE0.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE0.in>
# main:    Reading header from 1PV4_003_acc-PE1.dx...
# main:    Reading header from 1PV4_003_acc-PE1.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE1.in>
# main:    Reading header from 1PV4_003_acc-PE2.dx...
# main:    Reading header from 1PV4_003_acc-PE2.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE2.in>
# main:    Reading header from 1PV4_003_acc-PE3.dx...
# main:    Reading header from 1PV4_003_acc-PE3.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE3.in>
# main:    Reading header from 1PV4_003_acc-PE4.dx...
# main:    Reading header from 1PV4_003_acc-PE4.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE4.in>
# main:    Reading header from 1PV4_003_acc-PE5.dx...
# main:    Reading header from 1PV4_003_acc-PE5.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE5.in>
# main:    Reading header from 1PV4_003_acc-PE6.dx...
# main:    Reading header from 1PV4_003_acc-PE6.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE6.in>
# main:    Reading header from 1PV4_003_acc-PE7.dx...
# main:    Reading header from 1PV4_003_acc-PE7.in...
Vgrid_readDXhead:  Format problem with input file <1PV4_003_acc-PE7.in>
# main:   Dimensions of the merged grid
# main:   nx = 193, ny = 225, nz = 225
# main:   hx = 0.872922, hy = 0.622143, hz = 0.662777
# main:   xmin = -77.519, ymin = -63.158, zmin = -68.465
# main:   xmax = 90.082, ymax = 76.202, zmax = 79.997
# main:   Reading and Merging...
# main:    Reading data from 1PV4_003_acc-PE0.dx...
# main:    Merging data from 1PV4_003_acc-PE0.dx...
# main:    MIN (-77.519,-63.158,-68.465) IMIN (-78.0411,-63.5296,-68.8609)
# main:    MAX (6.02044,6.33619,5.56806) IMAX (6.54256,6.70782,5.96396)
# main:    Reading data from 1PV4_003_acc-PE0.in...
Vgrid_readDX:  Format problem with input file <1PV4_003_acc-PE0.in>
# main:    Merging data from 1PV4_003_acc-PE0.in...
# main:    MIN (-77.519,-63.158,-68.465) IMIN (-78.0411,-63.5296,-68.8609)
# main:    MAX (6.02044,6.33619,5.56806) IMAX (6.54256,6.70782,5.96396)
Bus error

The header is identical to the header in the .dx files for the potential from 'write pot dx', so I'm not sure what the problem is. The header for one of the files is:

# Data from APBS 0.5.0
#
# SOLVENT ACCESSIBILITY -- MOLECULAR (3.500 PROBE)
#
object 1 class gridpositions counts 161 188 188
origin -7.751900e+01 -6.315800e+01 -6.846500e+01
delta 5.221215e-01 0.000000e+00 0.000000e+00
delta 0.000000e+00 3.716267e-01 0.000000e+00
delta 0.000000e+00 0.000000e+00 3.958987e-01
object 2 class gridconnections counts 161 188 188
object 3 class array type double rank 0 items 5690384 data follows
1.000000e+00 1.000000e+00 1.000000e+00
1.000000e+00 1.000000e+00 1.000000e+00
1.000000e+00 1.000000e+00 1.000000e+00
1.000000e+00 1.000000e+00 1.000000e+00
1.000000e+00 1.000000e+00 1.000000e+00
1.000000e+00 1.000000e+00 1.000000e+00 


Any suggestions would be most appreciated.

Josh

 
------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group              Lab: 510.643.2159
218 Wellman Hall                                Fax: 510.642.7428
University of California, Berkeley     http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA                   jadelman@berkeley.edu
------------------------------------------------------------------------------------------------------