errors when I run find_pair

[shabeir]

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

[xiangjun]

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?

echo $X3DNA
find_pair -h

HTH,

Xiang-Jun

[shabeir]

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

[xiangjun]

It's likely. Could you post an example?

Xiang-Jun

[shabeir]

I am attaching my input pdb file and the results I got.

[xiangjun]

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:

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

[shabeir]

Thanks for your careful checking!
This is a type of 5' terminal patch in CHARMM force field.
Beibei