Abusaund,

 

After some digging and some offline discussions with Nathan we’ve concluded that the main problem is that specifying ADE in a PDB file is ambiguous. We don’t have enough information to determine if you are referring to DNA or RNA. The way the topology happens to be setup in PDB2PQR it behaves as though you are referring to an RNA sequence. It’s a bug, just not the bug I thought when I first responded to this.

 

To get the behavior you appear to want use DA instead of ADE. PDB2PQR will not add O2’ to your results this way. (Yes, Nathan, I tested it!)

 

Going forward we will probably remove ADE, CYT, GUA, THY, and URA (and A,C,G,T,U respectively) as residues accepted by PDB2PQR to eliminate this problem.

 

Kyle

 

From: Baker, Nathan
Sent: September 16, 2012 11:02
To: Monson, Kyle E; Abusaud; apbs-users@googlegroups.com
Cc: (apbs-users@lists.sourceforge.net)
Subject: RE: [apbs-users] O2' atom to DNA (PDB2PQR)

 

Hi Kyle --

 

Your analysis seems to be correct:  only the RNA versions of ADE (and guanine, cytosine, uracil) should have the O2'.  Can you clean up the patches for these?

 

Thanks!

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://nabaker.me

 


From: Monson, Kyle E
Sent: Friday, September 14, 2012 7:22 PM
To: Baker, Nathan; Abusaud; apbs-users@googlegroups.com
Cc: (apbs-users@lists.sourceforge.net)
Subject: RE: [apbs-users] O2' atom to DNA (PDB2PQR)

Nathan,

 

I think this is a bug.

 

You’ll have to pardon some of my ignorance of biochemistry in my explanation. I’ll over explain everything so you can point out where I run off the rails.

 

Based on a comment in the code (and some googling) the difference between DNA and RNA in this case is the presence of O2’. Having an O2’ means that it is RNA, however we list O2’ in the definition for ADE. As we don’t have any exceptions for this in the heavy atom code it gets added in.

 

I see an entry for RA based on A in patches.xml.  If this is for the RNA version of ADE then it looks like ADE and possibly some residue based on it are setup wrong.

 

I think we need to remove O2’ from ADE, change the RA patch to add it back in, change the DA patch to not remove it (it would already be gone), and change the RA3 and RA5 patches to be based on RA instead of A.

 

Let me know if this looks correct.

 

Kyle

 

From: Baker, Nathan
Sent: September 12, 2012 19:15
To: Abusaud; apbs-users@googlegroups.com
Cc: Monson, Kyle E; (apbs-users@lists.sourceforge.net)
Subject: RE: [apbs-users] O2' atom to DNA (PDB2PQR)

 

Hi Abusaud –

 

I passed this problem along to Kyle Monson for investigation.

 

Thanks,

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me

 

From: Abusaud [mailto:abusaude@gmail.com]
Sent: Tuesday, September 11, 2012 11:40 AM
To: apbs-users@googlegroups.com
Subject: [apbs-users] O2' atom to DNA (PDB2PQR)

 

I tried to convert ssAAA.pdb to pqr. I found there is an O2 atom added.

 

Could you pleases tell me if this process right or no.

 

I am attaching the pdb and pqr files.

 

 

---------------stdout.txt---------------

Checking for missing heavy atoms... 
        Missing O2' in ADE D 1
        Missing O2' in ADE D 2
        Missing O2' in ADE D 3
Missing 3 out of 63 heavy atoms (4.76 percent) - Will attempt to repair.
Rebuilding missing heavy atoms... 
        Added O2' to ADE D 1 at coordinates -4.519 4.960 -2.165
        Added O2' to ADE D 2 at coordinates -6.415 1.521 1.299
        Added O2' to ADE D 3 at coordinates -5.868 -2.290 4.844
Done.