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Author Topic: errors when I run find_pair  (Read 4449 times)

Offline shabeir

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errors when I run find_pair
« on: February 06, 2014, 01:44:23 pm »
Hello,
I want to do some analysis with x3dna-v2.1. At first I met the problem: open_file </home/user/x3dna-v2.1/BASEPARS/misc_3dna.par> failed: No such file or directory, and I changed the directory name from config to BASEPARS. But another error came: error reading upper HB criteria/alternative indicator. I do not know how to solve it. Can anyone help me?
Beibei

Offline xiangjun

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Re: errors when I run find_pair
« Reply #1 on: February 06, 2014, 01:52:05 pm »
It seems your 3DNA setup is at fault. See the post "How to install 3DNA on Linux and Windows?" for more details.

What does the following commands give?

Quote
echo $X3DNA
find_pair -h

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline shabeir

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Re: errors when I run find_pair
« Reply #2 on: February 06, 2014, 02:06:46 pm »
Thank you! I figured out that.
But I still have another problem.
It says: more than one  O5' atoms : residue name 'CYT', chain A, number    *****the first atom is used*****
But in my pdb file, i just have one O5' atom. I use 5PHO patch for the 5' terminal, is the O5T atom identified as another O5' atom.
Beibei

Offline xiangjun

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Re: errors when I run find_pair
« Reply #3 on: February 06, 2014, 02:15:56 pm »
It's likely. Could you post an example?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline shabeir

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Re: errors when I run find_pair
« Reply #4 on: February 06, 2014, 02:23:15 pm »
I am attaching my input pdb file and the results I got.

Offline xiangjun

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Re: errors when I run find_pair
« Reply #5 on: February 06, 2014, 02:42:19 pm »
Thank for providing a sample PDB file which helps clarify the issue.

Code: [Select]
ATOM      5  O1P CYT A   1      17.752  35.775  26.807  1.00  1.70      N01A
ATOM      6  O2P CYT A   1      17.012  35.542  24.381  1.00  1.70      N01A
ATOM      7  O5' CYT A   1      18.906  34.140  25.293  1.00  1.77      N01A
ATOM      8  O5T CYT A   1      19.074  36.580  24.990  1.00  1.77      N01A
Yes, it is the O5T [8, atom serial number]  which is taken as O5' by the 'analyze' program. Since the CYT #1 on chain A already has an O5' atom [7], that explains the message:
Quote
more than one  O5' atoms : residue name 'CYT', chain A, number [   1 ]
   *****the first atom is used*****
In your case, the assumption of taking the 1st O5' atom [7] in calculations works fine.

Which software did you use? This is the first time I noticed such an O5T naming. Presumably, O5T [8] should be the O3' atom in the preceding (5') nt. Here O5' [7] could be named O5T, which 3DNA handles without any problem.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline shabeir

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Re: errors when I run find_pair
« Reply #6 on: February 06, 2014, 03:46:01 pm »
Thanks for your careful checking!
This is a type of 5' terminal patch in CHARMM force field.
Beibei

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.