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Author Topic: Unknown residue DC  (Read 4338 times)

Offline alokjain

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Unknown residue DC
« on: September 13, 2008, 01:19:44 am »
Dear All,

I was trying to run the find_pair program to produce *.inp file. But I am encountering the following error.

unknown residue  DC    1  on chain A [#1]
Check the base and add one more item in file <baselist.dat>


I was executing the command find_pair -t 123D.pdb 123D.inp . It has all the normal base pairs. I have also checked the BASEPAIR.dat file. If I add the following lines in that file, then the program works fine.

 DA     A
 DC     C
 DG     G
 DT     T

These are normal base pairs, So I thought I do not have to modify the file. I have ~500 PDB files and all of them have similar problem.

I want to ask from you whether what I am doing is right or not by modifying the basepair.dat file or perhaps I am missing something.

Eagerly awaiting your reply.

Thanks & regards,
Alok Jain

Offline ghzheng

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Re: Unknown residue DC
« Reply #1 on: September 16, 2008, 04:32:59 pm »
Hi,

I would suggest you look through the Q&As, where you should be able to find that this issue has been raised before. This is due to a recent update of pdb format by the Protein Data Bank (as I remember, at the end of last year?). In the new format, bases DA, DT, DC, and DG are specified for DNA, while A, T, C, and G for RNA.

What you can do is:

1. Go the the 3DNA folder at where you installed.
2. Find the subfolder BASEPARS, and get in.
3. Open the file baselist.dat. In the file you will see basically two columns of residue names.
4. At the bottom of the file, add
DA      A
DT      T    
DC      C
DG     G

5. Save the file

Retry find_pair, and you should be fine.

Hope it works!

Guohui Zheng

 

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.