Re: [apbs-users] PDB2PQR running status

[Rohitesh G. <roh...@bu...>]

Kyle,

Thank you for the response. 
I am attaching here 2 links that are still running. Prior to this, there was another link for apbs calculation (same pdb file but without ligand) that resulted in some error. 

pdb2pqr links:
http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/querystatus.cgi?jobid=14007299453&apbsinput=True&calctype=pdb2pqr
http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/querystatus.cgi?jobid=14006993263&apbsinput=True&calctype=pdb2pqr

apbs link error:--> -->
 
 
<type 'exceptions.IOError'>	Python 2.7.3: /opt/python/bin/python2.7
Thu May 22 09:44:55 2014
A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/pdb2pqr_1.9.0/querystatus.cgi in ()
    621         from ZSI.TC import String
    622     else:
    623         have_opal = False
    624 
=>  625     mainCGI()
mainCGI = <function mainCGI>
 /var/www/html/pdb2pqr_1.9.0/querystatus.cgi in mainCGI()
    330             pdb2pqrJobIDFile.close()
    331         elif form["calctype"].value=="apbs":
=>  332             apbsJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value))
    333             jobid = apbsJobIDFile.read()
    334             apbsJobIDFile.close()
apbsJobIDFile undefined, builtin open = <built-in function open>, global INSTALLDIR = '/opt/pdb2pqr_1.9.0/', global TMPDIR = 'tmp/', global form = FieldStorage(None, None, [MiniFieldStorage('jobi...5387302'), MiniFieldStorage('calctype', 'apbs')]), ].value = [MiniFieldStorage('jobid', '14005387302'), MiniFieldStorage('calctype', 'apbs')]
<type 'exceptions.IOError'>: [Errno 2] No such file or directory: '/opt/pdb2pqr_1.9.0/tmp/14005387302/apbs_opal_job_id' 
      args = (2, 'No such file or directory') 
      errno = 2 
      filename = '/opt/pdb2pqr_1.9.0/tmp/14005387302/apbs_opal_job_id' 
      message = '' 
      strerror = 'No such file or directory'


Thanks,
Rohitesh



On May 22, 2014, at 10:49 AM, Monson, Kyle E wrote:

> Rohitesh,
> 
> It should not be much slower that a normal run. I can look into it.
> 
> Could you please send us the ligand and pdb file used to do this run. Could you also let us know what settings you are using.
> 
> If you still have the link to the status window for  the run that might be helpful also.
> 
> Thanks,
> Kyle
> 
> -----Original Message-----
> From: Rohitesh Gupta [mailto:roh...@bu...] 
> Sent: Wednesday, May 21, 2014 18:43
> To: apb...@li...
> Cc: apb...@go...; Baker, Nathan
> Subject: [apbs-users] PDB2PQR running status
> 
> Dear Team,
> 
> Any clue about the time PDB2PQR server takes in generating .pqr and .in files from protein and parameterized ligand, together? 
> 
> In the first case, pdb1 file was used containing only protein and the results were out within few minutes. 
> In the second case, another file (pdb1' ) for the same protein was used containing (protein+ligand). From this, protein was removed and the ligand was saved as MOL2 file.
> 
> To generate pqr file for this protein, I then used pdb1 and MOL2 file corresponding to the ligand generated from pdb1'. It's been over 8 hours and the results are still not out?
> Did anything went wrong here?
> 
> Thanks,
> Rohitesh
> 
> 
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users