Messages

1

MD simulations / Re: local helical axis vector for strongly bent DNA

« on: June 27, 2017, 04:44:07 pm »

Hello Xiang-Jun,

thank you very much for your detailed answer and your patience. This indeed helps me, and I understand that changing the criteria does not help in these cases.

So for everyone having the same problem, I used the following code:

Code: [Select]

find_pair myframe.pdb myframe.inpthis will create a file 'myframe.inp', which I modified in the way Xiang-Jun suggested in the answer above. Then

Code: [Select]

analyze myframe.inpcreates a file myframe.out with the results for all base-pairs including the broken one.
This worked in all cases so far, I will attach pictures of the problematic base-pairs of two more frames. I attached two pictures of the Frame72614_2 because it's not very clear to see, what is happening there in the first picture. The bases are not too far away from each other, but probably twisted too much.


Thank you again,
Adina

2

MD simulations / Re: local helical axis vector for strongly bent DNA

« on: June 26, 2017, 02:37:30 pm »

Hi Xiang-Jun,

thank you for your answer. I still couldn't figure out a way, so that base-pairs are recognized, even if they are broken. Since I have a long trajectory, editing the 'find_pair'-generated base-pair file is maybe not the best option in this case.

I tried altering the criteria, but somehow there are still base-pairs not recognized, although I changed the criteria to quite high values. I will attach a few frames, with which I have problems. Do you know, what I did wrong? In those frames are broken base-pairs, but it should be possible to still match them, I think.

The criteria I changed were the following:
Section 3: for find_pair program
#   maximum distance between base origins  (was 15 originally)
<max_dorg>40.0</max_dorg>

#   maximum vertical base separation, i.e., |stagger|  (was 2.5 originally)
<max_dv>20</max_dv>

#   maximum angle between base normals (in range 0..90)  (was 65 originally)
<max_plane_angle>90.0</max_plane_angle>

#   minimum distance between RN9/YN1 base atoms   (was 4.5 originally)
<min_dNN>1</min_dNN>

#   distance criterion for helix break   (was 7.8 originally)
<helix_break>50</helix_break>


Thank you very much for your time and your help,
Adina

3

MD simulations / Re: local helical axis vector for strongly bent DNA

« on: June 21, 2017, 08:28:25 pm »

Thank you very much, I was searching for something like this.

I have one more question.
Is there any possibility to find out, which of those criteria was the one, which caused, that the bases were not matched as pair? And can I find out what values those geometric quantities have?
Because then it would be easier to adjust the criteria in a way that all base-pairs are treated as such.

Thank you,
Adina

4

MD simulations / Re: local helical axis vector for strongly bent DNA

« on: June 21, 2017, 01:11:49 pm »

Hi Xiang-Jun,

thanks a lot for your fast reply! And sorry for not attaching the files.
I used the following command 

Code: [Select]

find_pair F29.pdb stdout | analyzeThe results, I get with that are F29-analyze.out and F30-analyze.out

The command you suggested, helps in the case of F29, where the '----' lines are calculated now (F29-analyze-c.out), but there is no change for F30.

The problem is, that this DNA has 10 base-pairs, but in F29-analyze.out it says, there are 9 base-pairs (And in F30-analyze.out it says there are 8 base-pairs). Why does X3DNA not recognize one (two) of the base-pairs?

Thanks for your help,
Adina

5

MD simulations / local helical axis vector for strongly bent DNA

« on: June 20, 2017, 06:49:53 pm »

Hello everyone,

I was analyzing a molecular dynamics simulation (http://www.amber.utah.edu/FF-DNA-bsc1-OL15/3GGI/opc/bsc0/ ) with do_x3dna and noticed, that in the HelAxis_g.dat file for most of the frames one line of data is missing. (sometimes even two lines are missing or replaced by '----'). The DNA contains 10 base-pairs, so there should be 9 helical axis vectors, since they are calculated as base-step parameters.

When I run single frames of the simulation with X3DNA, and look at the local helical axis vector there, I find four different cases.
1. "number of base-pairs: 10" ;  all helical axis vectors are calculated.
2. "number of base-pairs: 9"  ; the helical axis vector for one base-pair step is missing.
3. "number of base-pairs: 8"  ; the helical axis vectors for two base-pair steps are missing.
4. "This structure has broken O3'(i) to P(i+1) linkages"  and   "number of base-pairs: 9"  ; 
     the helical axis vector of one base-pair step is missing and in another line the data is replaced by '----'.

My explanation for this is, that if the program detects a broken base-pair, it refuses to calculate any vectors and prints '----' instead. Also it seems, that if the DNA is deformed or broken too much, then the program doesn't recognize this as a base-pair anymore and thinks the DNA is shorter than it actually is.

My question is now: Is there any way to force the program to still calculate a helical axis vector, even if the DNA is strongly bent and/ or broken?
And if yes, does maybe someone know, how to implement this into the do_x3dna program?

Thank you very much for your help,
Adina