Topics

1

RNA structures (DSSR) / human telomeric g quadruplex - base stacking energy

« on: November 08, 2017, 10:44:13 am »

Dear Xiang-Jun,


I wonder if 3DNA has an option to calculate the base pair stacking energy (projected area) for g-quadruplex RNA. I know 3DNA can do it for a dsDNA, but I wonder if there is the same option for g-quadruplex.

Thanks you,

Basilio.

2

General discussions (Q&As) / DNA FORM A/B

« on: July 21, 2017, 02:10:19 pm »

Dear Dr. Xiang-Jun Lu

I have a question, I could see that in the section Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases. in the output file there is a classification as A like or B-like. However, sometimes I see that the corresponding section appear empty. I copy my output to show you what I mean:

   8 GG/CC   -1.19    8.24    2.31   -9.23    7.09    4.72     A
   9 GG/CC   -1.30    8.29    1.93   -4.17    7.08    4.72     A
  10 GA/TC   -1.49    8.52    1.37   -2.55    8.53    1.31
  11 AG/CT   -1.31    8.33    2.80   -7.37    7.00    5.29     A
  12 GG/CC   -1.10    8.62    2.47   -3.32    8.96    0.43     A

Can you explain, please, what this mean for the software? I mean...I guess this is either not A or not B, what is this?

Thank you very much in advance,

Basilio.

3

MD simulations / How to generate a Methylated DNA pdb file from sequence to be use in MD

« on: June 23, 2017, 10:31:23 am »

Hello everyone,

I am new in this about MD using nucleic acid and I wonder, maybe this is a silly question, if there is a way to generate a pdb file from my dna sequence where some nucleotides are methylated, also I wonder if there are force field and parameter field available for them.

Thank you very much in advance,
Basilio.

4

General discussions (Q&As) / Minor and major grove calculation

« on: April 04, 2017, 11:02:42 pm »

Dear Xiang-Jun,

I would like to understand why I got this output when I calculated the minor and major groove from my pdb. It seems that there is some miss values. I attached the pdb I used (I am using 3DNA v2.0)

Thanks you in advance,

Basilio.

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 AA/TT       ---       ---       ---       ---
   2 AA/TT       ---       ---       ---       ---
   3 AA/TT       9.2       ---      20.8       ---
   4 AA/TT       9.2       9.1      21.1      21.1
   5 AA/TT       9.6       ---      20.1       ---
   6 AA/TT       ---       ---       ---       ---
   7 AA/TT       ---       ---       ---       ---
   8 AA/TT       ---       ---       ---       ---
   9 AA/TT       ---       ---       ---       ---
  10 AA/TT       ---       ---       ---       ---
  11 AA/TT      10.9       ---      19.3       ---
  12 AA/TT      10.6      10.3      18.7      18.4
  13 AA/TT       9.9       9.7      19.5      19.2
  14 AA/TT      10.4      10.3      20.7      20.7
  15 AA/TT      10.6       ---      18.7       ---
  16 AA/TT       ---       ---       ---       ---
  17 AA/TT       ---       ---       ---       ---

5

General discussions (Q&As) / Analysis of dna shape in methylated DNA

« on: April 04, 2017, 08:30:33 pm »

Hello,

I hope this email finds you well. I have a question. I got some DM trajectories of methylated GC dsDNA. When I tried to use the command "find_pair mypdb stdout | analyze" to calculate shape parameters I received the next message: unknown residue  DM    2  on chain A [#2]. Then what I did is to change the name (in mypdb) of the residue from DM to DC (Because the DM is methylated cytosine) and the command ran without problem. My logic was that since the methylation is not affecting the base pair, and I am interested to get the propeller twist, I can get correct values of the propeller twist. Is this correct?

Thank you,

Basilio.

6

MD simulations / "Ruby in cygwin"

« on: March 17, 2017, 07:15:59 pm »

Hello! My name is Basilio

I am trying to use 3DNA to analyze some MD data. I tried to do it with x3dna v2.0 (32) but it seems that this option is available just in x3dna v2.3....however, when I tried to install this in cygwin64...everything was ok till the computer told me that the problem is 'RUBY' I tried to install it but I did not find how to install ruby in cygwin64.... i really will appreciate your advice

Thank you,

Basilio.

7

General discussions (Q&As) / "Running 3DNA in cygwin64"

« on: March 16, 2017, 07:41:18 pm »

Hello,

I am Basilio Cieza. I have a question. I download 3DNA without problems, I download cygwin64 already and I followed the steps you suggested in a previous related question (http://forum.x3dna.org/howtos/how-to-install-3dna-on-cygwin-windows/msg2288/#msg2288) which suggest that everything is going well. However, I do not know if the installation was correctly done or not. I try to follow this manual (http://www.csb.yale.edu/userguides/datamanip/3dna/x3dna.pdf) but it seems that the commands like "find_pair pde0128.pdb pde0128.inp" are not working. I receive the message the command does not exist when I tried  to run it. I will really appreciate your advice.

Thank you so much,

Basilio