VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Thu Feb 17 2005 - 08:24:07 CST

You see the pot.dx file in /tmp because you didnt choose the working
directory. If you take a look at the graphical interface on the APBS
plugin you will see a place where you have to set the working directory
and the path of the APBS software.
Coloring: if you want to map the EP on a MSMS surface than set
representation as MSMS and color it as Volume: if you go to trajectory
under Graphics-Representations you can set the min and max of color
scale which yoou should choose from Graphics-Colors-Coilor scale
                 if you want isosurfaces ..you have to create 2...one
for min EP and one for max EP. Color them as color id (1 and 0 for
instance) and then you can vary the isovalue.
Hope this helps

Armen Nalian wrote:

>On the website http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/main.html
>it says that the plugin will present a list of any maps created by APBS upon
>its completion. I see the pot.dx file in the /tmp and when I load it onto
>psf and dcd I can see the isosurface but I am not sure what coloring method
>to choose (I don't see potential coloring method).
>Thank you,
>
>Armen
>-----Original Message-----
>From: Vlad Cojocaru [mailto:Vlad.Cojocaru_at_mpi-bpc.mpg.de]
>Sent: Thursday, February 17, 2005 3:33 AM
>To: nalianarmen_at_sfasu.edu
>Subject: Re: vmd-l: APBS error
>
>Did you look at the output?? Does it look properly. These errors look
>like ones that come from the differences in input lists from different
>APBS versions!
>However they do not affect the output of APBS.
>I am not completely sure if this is the case here but it looks like it
>is. Please check carefully the output and if you see a reasonable one,
>than I think you should not worry about these errors.
>vlad
>
>Armen Nalian wrote:
>
>
>
>>Dear all,
>>I tried to run apbs and got this error message by the end of the run.
>>I am using dcd structure and .psf file as input.
>>Thank you,
>>
>>Got PQR paths for 1 molecules
>>Reading PQR-format atom data from /tmp/ionized.pqr.
>> 41504 atoms
>> Centered at (-1.700e-02, 1.550e-02, -5.000e-02)
>> Net charge 3.99e-16 e
>>Preparing to run 2 PBE calculations.
>>----------------------------------------
>>CALCULATION #1: MULTIGRID
>> Setting up problem...
>> Vpbe_ctor: Using max ion radius (2 A) for exclusion function
>> Debye length: 7.8566 A
>> Current memory usage: 444.068 MB total, 444.068 MB high water
>> Using cubic spline charge discretization.
>> Grid dimensions: 129 x 129 x 129
>> Grid spacings: 1.005 x 0.745 x 0.925
>> Grid lengths: 128.630 x 95.412 x 118.432
>> Grid center: (-0.017, 0.016, -0.050)
>> Multigrid levels: 6
>> Molecule ID: 1
>> Linearized traditional PBE
>> Single Debye-Huckel sphere boundary conditions
>> 2 ion species (0.150 M ionic strength):
>> 2.000 A-radius, 1.000 e-charge, 0.150 M concentration
>> 2.000 A-radius, -1.000 e-charge, 0.150 M concentration
>> Solute dielectric: 1.000
>> Solvent dielectric: 78.540
>> Using "molecular" surface definition; harmonic average smoothing
>> Solvent probe radius: 1.400 A
>> Temperature: 298.150 K
>> Surface tension: 0.105 kJ/mol/A^2
>> Solving PDE (see io.mc* for details)...
>>----------------------------------------
>>CALCULATION #2: MULTIGRID
>> Setting up problem...
>> Vpbe_ctor: Using max ion radius (2 A) for exclusion function
>> Debye length: 7.8566 A
>> Current memory usage: 439.920 MB total, 531.934 MB high water
>> Using cubic spline charge discretization.
>> Grid dimensions: 129 x 129 x 129
>> Grid spacings: 0.670 x 0.497 x 0.617
>> Grid lengths: 85.753 x 63.608 x 78.954
>> Grid center: (-0.017, 0.016, -0.050)
>> Multigrid levels: 6
>> Molecule ID: 1
>> Linearized traditional PBE
>> Boundary conditions from focusing
>> 2 ion species (0.150 M ionic strength):
>> 2.000 A-radius, 1.000 e-charge, 0.150 M concentration
>> 2.000 A-radius, -1.000 e-charge, 0.150 M concentration
>> Solute dielectric: 1.000
>> Solvent dielectric: 78.540
>> Using "molecular" surface definition; harmonic average smoothing
>> Solvent probe radius: 1.400 A
>> Temperature: 298.150 K
>> Surface tension: 0.105 kJ/mol/A^2
>> Potential to be written to pot.dx
>> Solving PDE (see io.mc* for details)...
>> Writing potential to pot.dx
>>----------------------------------------
>>CLEANING UP AND SHUTTING DOWN...
>>Destroying force arrays.
>>No energy arrays to destroy.
>>Destroying multigrid structures.
>>Destroying 1 molecules
>>Final memory usage: 0.000 MB total, 531.934 MB high water
>>
>>
>>Thanks for using APBS!
>>
>>apbsrun: error occurred while running APBS:
>> parsePBE: Warning -- parsed deprecated "bcfl 1" statement
>>parsePBE: Please use "bcfl sdh" instead.
>>parsePBE: Warning -- parsed deprecated "srfm 1" statement.
>>parsePBE: Please use "srfm smol" instead.
>>NOsh: Warning -- parsed deprecated statment "chgm 1".
>>NOsh: Please use "chgm spl2" instead!
>>parsePBE: Warning -- parsed deprecated "calcenergy 0" statement.
>>parsePBE: Please use "calcenergy no" instead.
>>parsePBE: Warning -- parsed deprecated "calcforce 0" statement.
>>parsePBE: Please use "calcforce no" instead.
>>asc_getToken: Error occurred (bailing out).
>>Vio_scanf: Format problem with input.
>>
>>
>>
>>
>>
>>
>
>
> 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204