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Questions and answers => MD simulations => Topic started by: bratarajghosh on November 29, 2016, 08:56:37 am

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Title: x3dna_ensemble analysis error
Post by: bratarajghosh on November 29, 2016, 08:56:37 am
Hi everyone,

I just started learning the tool and facing a problem. When I am trying to do ensemble analysis this error is coming

any suggestion for what to do?

nsengupta@localhost:~/bg/DNA_project/100AAD/nxt$ x3dna_ensemble analyze -b tm_AAD_20-25ns.bps -e tm_AAD_20-25ns.pdb
        tm_AAD_20-25ns.pdb: with model numbers <= 0
Process model #0        1 / 9
/home/nsengupta/x3dna-v2.3/lib/miscs.rb:47: warning: Insecure world writable dir /home/nsengupta in PATH, mode 040777
mismatch between base-pair info and model file

thanking you,
brataraj
Title: Re: x3dna_ensemble analysis error
Post by: xiangjun on November 29, 2016, 09:02:37 am
Hi,

Thanks for using 3DNA, and for posting your questions on the Forum.

Were you able to repeat the sample applications of x3dna_ensemble distributed with 3DNA?

Please provide a (minimal) reproducible example so others can see exactly where the problem is in your case. Lacking that, the error message "mismatch between base-pair info and model file" may give you a hint.

Best regards,

Xiang-Jun
Title: Re: x3dna_ensemble analysis error
Post by: bratarajghosh on November 29, 2016, 11:21:23 pm
Hi,
Thanks a lot for replying.
Yes it did worked with the example file provided.
I am attaching my .pdb extracted from the trajectory with this post.
I guess it might help you to point out the problem.
Thanking you,
Brataraj
Title: Re: x3dna_ensemble analysis error
Post by: xiangjun on November 29, 2016, 11:30:16 pm
Please also provide your "tm_AAD_20-25ns.bps" file, for reproducing your problem.

Xiang-Jun
Title: Re: x3dna_ensemble analysis error
Post by: bratarajghosh on November 30, 2016, 07:52:54 am
Hi,

The .bps file is attached here.

thanking you,
Brataraj
Title: Re: x3dna_ensemble analysis error
Post by: xiangjun on November 30, 2016, 08:17:26 am
Thanks. Now I can reproduce the issue you reported. 3DNA is working properly. The problem is due to wrong PDB formatting in your MODEL/ENDMDL-delineated coordinate file. Specifically pay close attention to the "MODEL " record. An excerpt from the PDB format document (http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#MODEL) is shown below:

Code: [Select]
Record:

MODEL

Contains: the model serial number when a single coordinate entry contains multiple structures
Notes:
Models are numbered sequentially beginning with 1.
If an entry contains more than 99,999 total atoms,
then it must be divided among multiple models.
Each MODEL must have a corresponding ENDMDL record.
In the case of an NMR entry the EXPDTA record states the number of model structures
that are present in the individual entry.

COLUMNS       DATA TYPE      CONTENTS                           
----------------------------------------------------------------------
 1 -  6       Record name    "MODEL "                                           

11 - 14       Integer        Model serial number



Example:

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL        1
ATOM      1  N   ALA     1      11.104   6.134  -6.504  1.00  0.00           N
ATOM      2  CA  ALA     1      11.639   6.071  -5.147  1.00  0.00           C
...
...
ATOM    293 1HG  GLU    18     -14.861  -4.847   0.361  1.00  0.00           H
ATOM    294 2HG  GLU    18     -13.518  -3.769   0.084  1.00  0.00           H
TER     295      GLU    18                                           
ENDMDL                                                             
MODEL        2
ATOM      1  N   ALA     1      11.304   6.234  -6.104  1.00  0.00           N
ATOM      2  CA  ALA     1      11.239   6.371  -5.247  1.00  0.00           C
...
...
ATOM    293 1HG  GLU    18     -14.752  -4.948   0.461  1.00  0.00           H
ATOM    294 2HG  GLU    18     -13.630  -3.769   0.160  1.00  0.00           H
TER     295      GLU    18                                           
ENDMDL                                                             
Please check carefully and make changes accordingly.

BTW, which software did you use to generate this non-compliant PDB file?

Xiang-Jun
Title: Re: x3dna_ensemble analysis error
Post by: bratarajghosh on November 30, 2016, 01:24:50 pm

I actually wrote a code to put MODEL/ENDMDL accordingly. So it was not proper then. Is there is any tool for that to do it precisely according to needs?
thankihg you,
Brataraj
Title: Re: x3dna_ensemble analysis error
Post by: xiangjun on November 30, 2016, 03:02:17 pm
The PDB format documentation on the MODEL record cited above should be simple, and clear enough. Specifically, note the following:


The first three lines in your attached tm_AAD_20-25ns.pdb file is as below:

Code: [Select]
CRYST1   48.948   49.064  281.957  90.00  90.00  90.00 P 1           1
MODEL   0
ATOM      1  H5T ADE N   1     -25.814 -39.473  16.900  0.00  0.00      N1
ATOM      2  O5' ADE N   1     -26.106 -38.561  16.824  0.00  0.00      N1

You have used "MODEL\t0" for the first model (where \t stands for the tab character).

Check yours vs. the examples provided in the documentation, you should be able to solve your own problem. Have a try and report back how it goes.

HTH,

Xiang-Jun
Title: Re: x3dna_ensemble analysis error
Post by: bratarajghosh on December 02, 2016, 12:14:32 am
Hi,

Thank you for pointing out the problem.

It is working now.

Brataraj

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University