VMD-L Mailing List

From: Fateme Sadat Emami (fe2_at_zips.uakron.edu)
Date: Wed May 07 2014 - 14:45:22 CDT

Dear Mahbod and vmd users,
Thanks for your response. I am actually trying the APBS trough vmd. When I
try to run the APBS plugin in vmd I get the error message:

APBSRUN: output files missing or unreachable

Then, I wanted to check if the APBS itself is working fine (as being a
potential associated problem). Trying to run the APBS executable (downloaded
the precompile version from the website) I get the error message:

dyld: Library not loaded: libmaloc.dylib

  Referenced from: /Users/amirvahid/Documents/APBS-1.4-osx/bin/apbs

  Reason: image not found

Trace/BPT trap: 5

Logout

Hence it sounds like the precompiled ABPS is not working and complaining for
a library file. I checked the lib folder and the libmaloc.dylib is actually
there but it is not executable. Changing the permissions is not helping too.

Thanks again and I would be very much appreciated for any hint on this.

Fateme

---------------------------------------------------
Fateme Sadat Emami, Ph.D.
Postdoctoral Fellow
Non-Equilibrium Research Centre (NERC)
Northwestern University
2145 Sheridan Road, Tech K231
Evanston, IL 60208
email: fatemesadat.emami_at_northwestern.edu
Web: http://www.nercenergy.com/people/researchers.html

From: Mahbod Hajighasemi <mahbod81_at_yahoo.com>
Date: Wednesday, May 7, 2014 at 10:47 AM
To: Fateme Sadat Emami <fe2_at_zips.uakron.edu>
Subject: Re: [apbs-users] Missing library on mac

Hi Fateme,

Try a simple solution that solved a number of issues I've had using APBS on
mac. The idea is to run the pymol (assuming you're running APBS as a pymol
plugin) in windows mode. First have Xquartz (X11) software installed and
then go to the "applications" folder on your computer, locate the "macpymol"
application and then simply rename it to "macpymolx11hybrid". You would
realize that when you run the pymol it appears like the pc version. You may
proceed to your normal APBS analysis if the problem is the common mac
incompatibility of the plugin. Hope it works.

Cheers,
Mahbod

Sent from my iPad

On May 6, 2014, at 8:54 PM, Fateme Sadat Emami <fe2_at_zips.uakron.edu> wrote:

> Dear APBS users,
> I have just installed the APBS software on my mac. All the folders (bin,
> include, lib, share) are made, However when I run the executable I get the
> error message that libmaloc.dylib library is missing (the file is physically
> existed in the lib folder though). Could you please help me with ethis. I am
> sure this must be a primitive problem :(
>
> Thank you
> Fatima
>
>
> ---------------------------------------------------
> Fateme Sadat Emami, Ph.D.
> Postdoctoral Fellow
> Non-Equilibrium Research Centre (NERC)
> Northwestern University
> 2145 Sheridan Road, Tech K231
> Evanston, IL 60208
>
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