Hello –

 

Are you running APBS in a directory where you have write permission?

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://nabaker.me

 

From: Daisyang [mailto:daisyang095@gmail.com]
Sent: Saturday, December 17, 2011 7:43 PM
To: apbs-users@googlegroups.com
Subject: [apbs-users] output error

 

Hi,I am learning to call APBS  separately (I mean not with pymol or any other visualization tools ) to get electrostatic potential outputfile ,

I am  really new to APBS, so I used the input file that pymol generated (pymol-generated.in) as a try, but APBS gave me errors saying problem opening visual socket pymol.dx,

pymol.dx is the output file, but I didn't know what went wrong, all I need to do is to feed APBS the pqr file and get the electrostatic potentials for the 

molecular surface points. could anybody give me some hints please ?

 

the input file is here 

 

 

#

# Note that most of the comments here were taken from sample

# input files that came with APBS.  You can find APBS at

# http://agave.wustl.edu/apbs/

# Note that APBS is GPL'd code.

#

read

    mol pqr d:\2ea3.pqr       # read molecule 1

end

elec

    mg-auto

    dime   129 129 129  # number of find grid points

                     # calculated by psize.py

    cglen   69.149197 62.991801 67.046302 # coarse mesh lengths (A)

    fglen   60.675998 57.054001 59.439001 # fine mesh lengths (A)

                     # calculated by psize.py

    cgcent 16.289999 25.576000 27.368501  # (could also give (x,y,z) form psize.py) #known center

    fgcent 16.289999 25.576000 27.368501  # (could also give (x,y,z) form psize.py) #known center

    lpbe               # solve the full nonlinear PBE with npbe

    #lpbe            # solve the linear PBE with lpbe

    bcfl sdh          # Boundary condition flag

                     #  0 => Zero

                     #  1 => Single DH sphere

                     #  2 => Multiple DH spheres

                     #  4 => Focusing

                     #

    #ion 1 0.000 2.0 # Counterion declaration:

    ion charge  1 conc 0.150000 radius 2.000000     # Counterion declaration:

    ion charge -1 conc 0.150000 radius 1.800000     # ion <charge> <conc (M)> <radius>

    ion charge  2 conc 0.000000 radius 2.000000     # ion <charge> <conc (M)> <radius>

    ion charge -2 conc 0.000000 radius 2.000000     # ion <charge> <conc (M)> <radius>

    pdie 2.000000          # Solute dielectric

    sdie 78.000000          # Solvent dielectric

    chgm spl2          # Charge disc method

                     # 0 is linear splines

                     # 1 is cubic b-splines

    mol 1            # which molecule to use

    srfm smol        # Surface calculation method

                     #  0 => Mol surface for epsilon;

                     #       inflated VdW for kappa; no

                     #       smoothing

                     #  1 => As 0 with harmoinc average

                     #       smoothing

                     #  2 => Cubic spline 

    srad 1.400000          # Solvent radius (1.4 for water)

    swin 0.3         # Surface cubic spline window .. default 0.3

    temp 310.000000          # System temperature (298.15 default)

    sdens 10.000000         # Specify the number of grid points per square-angstrom to use in Vacc object. Ignored when srad is 0.0 (see srad) or srfm is spl2 (see srfm). There is a direct correlation between the value used for the Vacc sphere density, the accuracy of the Vacc object, and the APBS calculation time. APBS default value is 10.0.

    #gamma 0.105      # Surface tension parameter for apolar forces (in kJ/mol/A^2)

                     # only used for force calculations, so we don't care, but

                     # it *used to be* always required, and 0.105 is the default

    calcenergy no    # Energy I/O to stdout

                     #  0 => don't write out energy

                     #  1 => write out total energy

                     #  2 => write out total energy and all

                     #       components

    calcforce no     # Atomic forces I/O (to stdout)

                     #  0 => don't write out forces

                     #  1 => write out net forces on molecule

                     #  2 => write out atom-level forces

    write pot dx pymol  # What to write .. this says write the potential in dx

                     # format to a file.

end

quit