[Apbs-users] ObjectMapLoadDXFile-Error

[Anderson, K. <kua...@ut...>]

Hello,

Yet another posting a DXfile error...sorry all.

I've spent some time going through the board here, and I believe I've done everything right by minimizing the path, eliminating spaces, etc...but to no avail.  I think the error is in the temp assignment--maybe a quick tip will get me going, thanks.  

-Kurtis Anderson



PyMOL>reinitialize 
 CmdLoad: "/Users/djroue/APBS/test2/1fas.pqr" loaded as "1fas".
 APBS Tools: set pqr file to /Users/djroue/APBS/test2/1fas.pqr
cs [4, 3, 4]
finedim [54.762001037597656, 41.559899234771727, 53.782000541687012]
nlev 4
mult_fac 32
finegridpoints [129, 97, 129]
Maximum number of grid points exceeded.  Old grid dimensions were [129, 97, 129]
Fine grid points rounded down from [117, 87, 117]
New grid dimensions are [97, 65, 97]
 APBS Tools: coarse grid: (59.095,41.560,57.429)
 APBS Tools: fine grid: (54.762,41.560,53.782)
 APBS Tools: center: (36.269,19.971,7.486)
 APBS Tools: fine grid points (97,65,97)
ObjectMapLoadDXFile-Error: Unable to open file!



=======================================================
GENERAL INFO
=======================================================
APBS 1.1.0 (Mac OS X Intel)
Mac OS X 10.4.11
working directory: /Users/djroue/APBS/test2/


APBS installed in:
/Applications/apbs-1.1.0/


PyMOL installed in:
/Applications/PyMOLX11Hybrid.app/ 



=======================================================
PyMOL APBS TOOLS
=======================================================
MAIN
Choose externally generated PQR:
/Users/djroue/APBS/test2/1fas.pqr

CONFIGURATION
Set grid - CLICKED
[ion] +1 = 0.150
[ion] -1 = 0.150

APBS LOCATION
APBS binary location:
/Applications/apbs-1.1.0/bin/apbs

TEMP FILE LOCATIONS
Temp PQR file: 
/Users/djroue/APBS/test2/pymol-generated.pqr

Temp PDB file:
/Users/djroue/APBS/test2/pymol-generated.pdb

Temp DX file:
/Users/djroue/APBS/test2/pymol-generated.dx

APBS input file:
/Users/djroue/APBS/test2/1fas.in.txt



=======================================================
APBS INPUT FILE (1fas.in.txt from PDB2PQR server)
=======================================================
read
    mol pqr 1fas.pqr
end
elec 
    mg-auto
    dime 129 97 97
    cglen 63.1108 45.7300 61.4601
    fglen 57.1240 45.7300 56.1530
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
    write pot dx pot
end
elec 
    mg-auto
    dime 129 97 97
    cglen 63.1108 45.7300 61.4601
    fglen 57.1240 45.7300 56.1530
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 2.0000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end
print elecEnergy 2 - 1 end
quit


=======================================================
PQR file: /Users/djroue/APBS/test2/1fas.pqr
=======================================================

REMARK   1 PQR file generated by PDB2PQR (Version 1.4.0)
REMARK   1
REMARK   1 Forcefield Used: parse
REMARK   1 Naming Scheme Used: parse
REMARK   1
REMARK   5
REMARK   6 Total charge on this protein: 4.0000 e
REMARK   6
ATOM      1  N   THR     1      46.148  16.581   2.104 -0.3200 2.0000
ATOM      2  CA  THR     1      44.862  15.936   2.105  0.3300 2.0000
ATOM      3  C   THR     1      43.983  16.642   1.087  0.5500 1.7000
ATOM      4  O   THR     1      44.150  17.855   0.925 -0.5500 1.4000
ATOM      5  CB  THR     1      44.293  16.088   3.528  0.0000 2.0000
ATOM      6  OG1 THR     1      45.409  15.915   4.403 -0.4900 1.4000
ATOM      7  CG2 THR     1      43.175  15.110   3.826  0.0000 2.0000
...
ATOM    910  HD1 TYR    61      30.649  12.920   7.128  0.1250 1.0000
ATOM    911  HB1 TYR    61      32.812  13.407   6.001  0.0000 0.0000
ATOM    912  HB2 TYR    61      32.833  13.922   4.451  0.0000 0.0000
ATOM    913  HH  TYR    61      26.611  13.103   3.935  0.4350 1.0000
HETATM  914  OH  H2O    62      27.026  18.812   4.463 -0.7200 1.4000
HETATM  915  HH1 H2O    62      27.025  19.769   4.172  0.3600 1.0000
HETATM  916  HH2 H2O    62      26.191  18.671   4.995  0.3600 1.0000
...
HETATM 1226  OH  H2O   166      29.627  27.168  24.722 -0.7200 1.4000
HETATM 1227  HH1 H2O   166      29.614  27.412  23.752  0.3600 1.0000
HETATM 1228  HH2 H2O   166      30.517  26.813  25.007  0.3600 1.0000






Kurtis Anderson
Keck Fellow - Structural Biology in Biodefense
Graduate Student - Biophysics, Structural and Computational Biology
University of Texas Medical Branch
Galveston, TX, 77555-1131
(409) 747-6815 work
(516) 661-3199 cell
kur...@ut...