no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat

[Asmita]

Dear Users,

   I am new to 3DNA suite of programs. I have a set of PDB coordinates generated using ptraj utility in Amber MD package. For the same i want to analyze base-step geometries. When i am running find_pair pdb-file pdb-file.inp and then analyze -c pdb-file.inp, an output file is generated , but when i am trying to do the same on multiple files using a shell script in a loop, i am getting this message :

-------------------------------------------------------------------------------------
no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat'
        now it is set as 'OP'
        check and update file $X3DNA/config/atomlist.dat
no matching entry for atom name [OP2 ] (OP..) in 'atomlist.dat'
        now it is set as 'OP'
        check and update file $X3DNA/config/atomlist.dat
no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat'
        now it is set as 'OP'
-----------------------------------------------------------------------------------
 and hence analyze doesn't give an output file, saying "can not read strand information"

i tried to manually add the OP1, OP2 and O1P, O2P entries in atomlist.dat, but still getting the same message. What am i missing here? an example PDB file is attached herewith...

Thanks

Asmita

[xiangjun]

Hi Asmita,

Thanks for joining the 3DNA-user community!

Posting your question on the forum is a good first step; attaching a specific example so that your problem can be reproduced is better still.

The problem is due to the non-standard format of your PDB file, as shown below:

# The following is extracted from your attached "struct_1.pdb"
ATOM     30 P    G       2      -3.465  14.386  -4.840  0.00  0.00
ATOM     31 OP1  G       2      -4.272  15.372  -4.078  0.00  0.00
ATOM     32 OP2  G       2      -2.267  13.805  -4.173  0.00  0.00
ATOM     17  P    DG A   2      23.337  31.278  21.156  1.00 13.26           P  
ATOM     18  OP1  DG A   2      24.761  31.571  21.391  1.00 13.17           O  
ATOM     19  OP2  DG A   2      22.651  31.834  19.956  1.00 12.34           O
# The above in red is taken from PDB entry 355d  
 

As you can see clearly, the atom name (and residue name) in your PDB file is shifted to the left by one column. So the atom name for OP1 is taken as

"OP1 " instead of the normal " OP1", 

and that explains the message you saw:

no matching entry for atom name [OP1 ] (OP..) in 'atomlist.dat'

Adding an entry "OP..   O" (note the two dots in place of digit and space) to file 'atomlist.dat' will make the info message go away.

The most effective way to fix such problems is to ensure your PDB file is standard compliant [see Coordinate File Description (PDB Format)]. In your case, ask the developers of your MD package to generate standard compliant PDB file, or you can write a simple script to make the changes. This is the first time I am aware of such problem; given enough interest, I will consider to refine 3DNA to accommodate such non-standard cases.

HTH,

Xiang-Jun

[Asmita]

Dr Lu

   Thanks for the response...As you suggested, i made the changes in the atomlist.dat file...Find_pair seems to be working fine, but when i am running analyze -c on .inp files, i am getting this message :

-----------------------------------------------------
......Processing structure #1: <1l2x_prod_run_1.inp>......
This structure has broken O3' to P[i+1] linkages
missing ' P  ' atom : residue name ' C5', chain  , number [   1 ]
missing ' O1P' atom : residue name ' C5', chain  , number [   1 ]
missing ' O2P' atom : residue name ' C5', chain  , number [   1 ]
missing ' O1P' atom : residue name '  G', chain  , number [   2 ]
missing ' O2P' atom : residue name '  G', chain  , number [   2 ]
missing ' O1P' atom : residue name '  C', chain  , number [   3 ]
missing ' O2P' atom : residue name '  C', chain  , number [   3 ]
missing ' O1P' atom : residue name '  G', chain  , number [   4 ]
missing ' O2P' atom : residue name '  G', chain  , number [   4 ]
missing ' O1P' atom : residue name '  G', chain  , number [   5 ]
missing ' O2P' atom : residue name '  G', chain  , number [   5 ]
missing ' O1P' atom : residue name '  C', chain  , number [  24 ]
missing ' O2P' atom : residue name '  C', chain  , number [  24 ]
missing ' O1P' atom : residue name '  G', chain  , number [  25 ]
missing ' O2P' atom : residue name '  G', chain  , number [  25 ]
missing ' O1P' atom : residue name ' G3', chain  , number [  26 ]
missing ' O2P' atom : residue name ' G3', chain  , number [  26 ]
missing ' O1P' atom : residue name '  G', chain  , number [  16 ]
missing ' O2P' atom : residue name '  G', chain  , number [  16 ]

..
.
.
.
--------------------------------------------------------------------------------

As there are lakhs of PDB files, instead of formatting these files, i tried to introduce these modifications in atomlist.dat :
------------------------
.
.
.
OP..   O        (for OP1,OP2 etc)
O.P.   O        (for O1P, O2P etc)
..OP   O        (in case some weird naming convention comes up)
-------------------------

but still analyze -c run fails saying that "couldn't handle strand information" with error message mentioned above..could you please suggest what can i do?

Thanks

Asmita

[xiangjun]

Okay, please download the 2012oct06 updated (beta) version of v2.1 and try again. The atom naming issues should have been resolved. Please report back whether reinstalling the revised version does help.

Xiang-Jun

[Asmita]

Dr Lu

    The issue i mentioned is coming in 2012 October beta v2.1 only...(for 64 bit ubuntu). As i am relatively new, i installed the latest version given in the downloads section in the first place....I am trying to reformat all the pdb files now...if it works then i'll post again


Asmita

[xiangjun]

Well, you have not yet downloaded the 2012oct06 updated version I just compiled to solve the naming issue you experiences (see What's new?). The file should be named: x3dna-v2.1-linux-64bit-2012oct06.tar.gz.

Xiang-Jun