[apbs-users] Unable to write dx file (permission problem?)

Grant Kemp

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Aug 29, 2016, 6:43:35 AM8/29/16

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Hi everyone,

I am having a hard time generating a .dx file from apbs. I am running both pdb2pqr (bin not source) and apbs (mac .app) locally because I am working with the ribosome, which is too big for the web servers. pdb2pqr seems to run fine and I generate both the .in and .pqr files without issue. However, when I run apbs it seems to work (it runs both calculations without generating any error messages until it goes to write the potential to the .dx file and gives the following:

Writing potential to input/Kemp17_01.pqr.dx

Vio_ctor2: some error occurred.

Vio_ctor: Vio_ctor2() failed.

Vgrid_writeDX: Problem opening virtual socket input/Kemp17_01.pqr.dx

Then is cleans up and says "Thank you". The first time it failed I noticed that the advice was that the permissions were probably not correct, but to address this I "chmod 777" the working directory and even one level up so now all the input files and the folder that the .dx file is being written to have -rwxrwxrwx permissions. Is this a problem with the install? I am using the latest apbs.dmg so I am running the mac app. I also had a problem with the library path but I corrected it using this advice: https://github.com/Electrostatics/apbs-pdb2pqr/issues/450 but maybe my problem is still somehow related to this. Thanks in advance for any advice!

Cheers,

Grant

Star, Keith

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Aug 29, 2016, 2:04:32 PM8/29/16

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Hi Grant,

I apologize for the obtuse error. I don't think that it's a problem with the install. How large is the PQR file, and what's the resolution you are using in the .in file? I'm wondering if it might not be a disk space issue? If you are willing, you could send me the PQR and .in file and I could try running it on my Mac.

Thanks,

- Keith

Grant Kemp

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Aug 29, 2016, 3:04:27 PM8/29/16

to Star, Keith, apbs-...@lists.sourceforge.net

Hi Keith,

I am a newbie and I am running everything with the default settings. I did not mean to make it sound like you were saying it was a problem with the install, maybe just where it pointed in the newer OS X. My little MacBook Pro only has 4Gb of memory and the ribosome is over 200,000 atoms so that might be an issue, but when I rerun apbs with a smaller pdb as a test (a modelled coiled-coil) it also fails. I am happy to provide you with the .in and .pqr files for this smaller one and you can let me know if there is something strange about my file preparation :)

Cheers,

Grant

From: Star, Keith <ke...@pnnl.gov>
Sent: 29 August 2016 20:03
To: Grant Kemp; apbs-...@lists.sourceforge.net
Subject: Re: [apbs-users] Unable to write dx file (permission problem?)

Grant Kemp

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Aug 30, 2016, 2:35:30 PM8/30/16

to Grant Kemp, apbs-...@lists.sourceforge.net

Update: Problem solved! It was issue with the write location for the .dx file. Because I ran the pdb2pqr from one directory higher, apbs was trying to write to a directory that did not exist. A simple edit in the .in file (as noted by Keith) fixed the problem. Thank you Keith!