trajectory analysis: error with analyze

[vmsrvignesh]

Dear All,

I am trying to analyze a 10 ns MD trajectory of a 12 bp DNA. I followed the instructions in the http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=1&t=75 as to create an analyze.inp file from a reference structure (here, I used the initial structure) and modify the first 2 lines for analyzing the rest of the simulation frames. However, at around 8 ns, I get the following error:

...... reading file: misc_3dna.par ......
some residue has more than one pair
residue index 24 too big (> 22)
please check your input file

On visually analyzing the structure, I do see some slight changes in the pairing, but I am not able to judge correctly which is why I decided to analyze using X3DNA.

Without any clue as to what this error might actually mean, I did the following too:

I made a new analyze.inp for the 8ns'th frame and re-did the find_pair function. The function finds only 9 bps!

Could anybody give me some pointers as to what this error might indicate and how to go about it?

Thank you,
Sincerely,
Vignesh

Grad Student,
Natl. Univ. of Singapore.

[vmsrvignesh]

Dear All,

I am so sorry. I figured out an error with my simulations - I hadn't taken care of PBC. So, after fixing it I no longer get the error I had mentioned.

However, I would still like to know a bit more about the error.

Any pointers would be greatly appreciated.

Thanks very much,
Vignesh

Grad Student,
Natl Univ of Singapore.

[xiangjun]

I figured out an error with my simulations - I hadn't taken care of PBC. So, after fixing it I no longer get the error I had mentioned.

However, I would still like to know a bit more about the error.

I am glad that you figured out where the problem was.

Regarding the meaning of the error message,

Code: [Select]

some residue has more than one pair
residue index 24 too big (> 22)
please check your input fileIt would help clarify the issue greatly if you include a minimal, producible example so others can understand exactly what you mean. Broadly speaking, it means the input file to analyze does not match the corresponding PDB file. More specifically, in your input file, a nucleotide is specified with sequential no. 24, while the PDB has only 22 residues.

HTH,

Xiang-Jun

[vmsrvignesh]

Thank you!

I had the following DNA sequence in my MD simulations: 5'-CGCGAATTCGCG-3' in a 10x10x10 nm^3 box with water.
I analyzed the MD trajectory for a 10ns simulation of the above system with 3DNA. Apparently, at one time point, the DNA had gone out of the box and so 3DNA had problems analyzing it. However, after fixing the "jump" of the DNA (i.e., on accounting for the Periodic Boundary Conditions), I had no problem using 3DNA to analyze the trajectory.

Thank you very much,
Vignesh

Grad. Student,
Natl. Univ. of Singapore,
Singapore.