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Author Topic: No matching entry in atomlist.dat  (Read 6928 times)

Offline shynomat

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No matching entry in atomlist.dat
« on: April 29, 2012, 07:49:24 pm »
Dear all,

I am trying to use find_pair as shown below:
find_pair -c+ sel.pdb new.inp
I am getting this error: no matching entry for atom name [  OW] (..OW) in 'atomlist.dat'
   now it is set as 'XX'
In my pdb file water is listed as OW. In this case should I add this as a new atom to atomlist.dat?
For the same analysis, I had to modify baselist.dat. The following bases were added:
DG3- 3 terminal guanine
DC5- 5 terminal cytosine

thanks
Shyno

Offline xiangjun

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Re: No matching entry in atomlist.dat
« Reply #1 on: April 29, 2012, 08:23:33 pm »
In the default 'atomlist.dat' file, there is an entry, [.OW.   O]. Presumably, yours should be added as: [..OW   O].

DG3 and DC5 have already been included in 'baselist.dat' (as 'g' and 'c' respectively). What specific message does 'find_pair' output for your structure? Did you know that, as of 3DNA v2.1, you do not have to modify 'baselist.dat'?  Nevertheless, it is a good idea to be explicit about each mapping.

Attaching a sample PDB file would clarify the issues.

Xiang-Jun
« Last Edit: April 29, 2012, 11:16:09 pm by xiangjun »

Offline shynomat

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Re: No matching entry in atomlist.dat
« Reply #2 on: May 02, 2012, 01:42:02 pm »
Hello Xiangjun,

thank you very much for your reply.
You are correct, I don't need to modify the baselist.dat, actually I got that message with v 1.5 which I tried first. Now I am using v2.1beta.
Regarding the "No matching entry in atomlist.dat", my pdb format was wrong! Once I fixed that issue, everything seems fine.
thanks again for your reply and sorry for the delay in replying.

Regards
Shyno

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.