Messages

1

General discussions (Q&As) / Re: using x3dna to analyze a coarse grained model mapped into an atomistic model

« on: March 03, 2016, 02:45:02 am »

Hi,

Sorry for the trouble.I have attached the .png, .alc and the .pdb file I do the analysis on.

Thanks!

2

General discussions (Q&As) / Re: using x3dna to analyze a coarse grained model mapped into an atomistic model

« on: March 02, 2016, 09:25:18 am »

Hello Dr. Xiang-Jun,

In order to get the helical axis I have used the rebuild command and every thing seems ok for the axis but there is something unusual in the image that I can not understand.It seems that some of the bases are elongated to a far distance!
I have attached the image (I use jmol to view it).
I was wondering if you could have a look at it and help me out!

Thanks in Forward

3

General discussions (Q&As) / Re: using x3dna to analyze a coarse grained model mapped into an atomistic model

« on: February 24, 2016, 09:20:15 am »

Dear Dr.Xiang Jun,

Thanks a lot for your reply.actually your point helped me to solve the problem.as the equilibrated base distance in the CG model (regarding the PMF analysis) is 7 A, I changed the default value from 4 to 7 and now all the bases are recognized.
I have some more questions:
1) is the periodic box information important for X3DNA in analysis of the structure.
2) regarding the data for groove analysis, it seems that the measured values are switched off for the minor and major groove (the values for the minor groove are bigger than the major groove).so I was wondering if you have any suggestions about this issue.

Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 GC/GC       ---       ---       ---       ---
   2 CC/GG       ---       ---       ---       ---
   3 CC/GG      20.6       ---      11.8       ---
   4 CC/GG      16.1      15.9      13.1      11.5
   5 CC/GG      16.3      15.8      11.8       9.7
   6 CC/GG      15.3      14.9      12.2      10.4
   7 CC/GG      15.0      14.8      12.3      11.3
   8 CC/GG      16.9      16.6      11.6      10.7
   9 CC/GG      18.4      17.8      12.0      10.9
  10 CC/GG      18.1      17.6      14.0      12.9
  11 CC/GG      17.8      17.6      13.2      12.4
  12 CC/GG      17.4      17.3      12.8      11.1
  13 CC/GG      16.8      16.6      12.9      10.7


again, thanks a lot for your help I really appreciate it.

4

General discussions (Q&As) / using x3dna to analyze a coarse grained model mapped into an atomistic model

« on: February 23, 2016, 10:36:59 am »

Hello,

I have a coarse grained DNA model(two bead model one for bases and the other for phosphates and sugar or backbone) and using NAB (from Amber) I have mapped it into an atomistic CG model. the primary structure is about 400 base pairs. when I feed it to X3DNA it just recognize 75 base pairs and not the rest.
I also receive the following   warnings after executing the code:
***Warning: structure with overlapped base-pairs***
This structure contains intra-chain direction reverse
(I have attached the pdb file of the model if you are interested to have a look).
 
Thanks in Forward for your help!