3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: NARENDRA on August 17, 2006, 09:00:47 pm

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Title: Missing P atom in first residues- error
Post by: NARENDRA on August 17, 2006, 09:00:47 pm
When I run X3DNA I get the following error. I do not have a phosphate group on the first residue, so can this error be ignored?

Residue 3 and 21 are first residues in each strand.

 ...... reading file: baselist.dat ......
missing " P  " atom : residue name   A, chain  , number    3
missing " P  " atom : residue name   A, chain  , number   21
Title: Re: Missing P atom in first residues- error
Post by: xiangjun on August 17, 2006, 09:53:49 pm
Dear NARENDRA,

Thanks for being the first 3DNA user to try out this forum!

No, these are not error messages -- they are there for information only, noting the fact that some atoms are missing from a base residue. In this case, you will find that some backbone torsion angles involving these atoms will be missing from the main output file.

For example, with bdl084, the output will be:


Code: [Select]
Strand I
  base    alpha    beta   gamma   delta  epsilon   zeta    chi
   1 C     ---     ---    -70.0   144.7  -171.8   -98.4  -105.9
   2 G    -69.8  -172.2    43.0   148.1  -151.3  -157.0   -85.4
   3 C    -39.4   130.5    50.1    93.3  -165.4   -81.2  -132.4


HTH,

Xiang-Jun

Quote from: "NARENDRA"
When I run X3DNA I get the following error. I do not have a phosphate group on the first residue, so can this error be ignored?

Residue 3 and 21 are first residues in each strand.

 ...... reading file: baselist.dat ......
missing " P  " atom : residue name   A, chain  , number    3
missing " P  " atom : residue name   A, chain  , number   21

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.