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:

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
=>  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 =
    334             apbsJobIDFile.close()
apbsJobIDFile undefinedbuiltin 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'


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


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.


-----Original Message-----
From: Rohitesh Gupta []
Sent: Wednesday, May 21, 2014 18:43
Cc:; 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?


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