Messages

1

MD simulations / Re: issues with x3dna_ensemble

« on: June 06, 2013, 12:08:40 pm »

sorry, the previous message got posted accidently. Since my system has 12 bp steps, it should have 11 inter base pair steps.
If it is not clear this is what I want inside sel.out if possible:
Local base-pair step parameters
          step        Shift      Slide      Rise       Tilt         Roll     Twist
   1  CG/CG       ---         ---         ---           ---         ----       ----     
   2  GC/GC      1.29      0.44      2.62       6.32      -3.86    31.01
   3  CG/CG     -1.11    -0.04      3.86      -6.40     14.10     35.74
   4  GA/TC       0.78    -0.30      3.57      -0.97       2.92     36.20
   5  AA/TT       -0.44    -0.77      3.48      -0.74       2.14     35.20
   6  AC/GT       0.00     0.04      3.09       2.14       0.76     39.12
   7  CG/CG      0.68     0.41      3.21      -2.61     17.38     29.80
   8  GC/GC      0.40    -0.35      3.28      -0.47       0.89     32.94
   9  CG/CG     -0.64     0.39      3.04       3.76       9.39     29.46
  10 GC/GC     -0.36    -0.89      3.40      -6.53       1.69     37.52
  11 CG/CG      0.93    -0.64      3.45       2.40     10.67     32.12
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.            0.15     -0.17      3.30     -0.31      5.61     33.91
      s.d.             0.78      0.50      0.34      4.16      6.84      3.33

2

MD simulations / Re: issues with x3dna_ensemble

« on: June 06, 2013, 11:58:35 am »

Hello Dr. Xianjun,
thanks again for your reply. I have another question related to this post.
As shown in the sel.out file clearly the first bp step 'CG' is missing, I was wondering if there is way to print out this step in the sel.out, even though it doesn't have any values associated with it. It would be very helpful for me to have all the bp steps listed all the time even if they don't have values associated with it.
For example, the section for inter base pair step parameters will look something like this:

   Local base-pair step parameters
    step            Shift     Slide      Rise      Tilt      Roll     Twist
   1. CG/CG  ---       
   1 GC/GC      1.29      0.44      2.62      6.32     -3.86     31.01
   2 CG/CG     -1.11     -0.04      3.86     -6.40     14.10     35.74
   3 GA/TC      0.78     -0.30      3.57     -0.97      2.92     36.20
   4 AA/TT     -0.44     -0.77      3.48     -0.74      2.14     35.20
   5 AC/GT      0.00      0.04      3.09      2.14      0.76     39.12
   6 CG/CG      0.68      0.41      3.21     -2.61     17.38     29.80
   7 GC/GC      0.40     -0.35      3.28     -0.47      0.89     32.94
   8 CG/CG     -0.64      0.39      3.04      3.76      9.39     29.46
   9 GC/GC     -0.36     -0.89      3.40     -6.53      1.69     37.52
  10 CG/CG      0.93     -0.64      3.45      2.40     10.67     32.12
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      ave.      0.15     -0.17      3.30     -0.31      5.61     33.91
      s.d.      0.78      0.50      0.34      4.16      6.84      3.33

3

MD simulations / Re: issues with x3dna_ensemble

« on: June 04, 2013, 10:52:47 pm »

Hello Xianjun,
thank you very much for the detailed message. I did these steps again and got the same results. In a way, I only need to do the following first two steps:
find_pair sel.pdb bpfile.dat
analyze bpfile.dat

as the sel.out contains all the information I need, correct. Just to make sure.

thanks,
Shyno

4

MD simulations / Re: issues with x3dna_ensemble

« on: June 04, 2013, 01:19:55 pm »

Thanks again for your reply. But I am only considering one frame. Please see the attached pdb file, bpfile.out and ensemble.out.
I would like to know if there is way to extract bp steps along with values for shift using 'x3dna_ensemble extract'.
I apologize if the previous question wasn't clear.
The following are the steps I used to create bpfile.dat, ensemble.out:
1. find_pair sel.pdb bpfile.dat
2. x3dna_ensemble analyze -b bpfile.dat -p sel.pdb -o ensemble.out
thanks,
Shyno

5

MD simulations / Re: issues with x3dna_ensemble

« on: June 04, 2013, 11:00:50 am »

Dear Dr. Xianjun,
Thanks again for your detailed message.
Regarding point #2, when you say "the serial number is used in ensemble.out for simplicity", I am little confused, in the sense I don't find seriel number corresponding to bp steps. For example, if I am interested in looking at the shift parameter, the line that has this info in the ensemble.out is:

<shift>   # with 10 data columns
sel 1.29  -1.11 0.78  -0.44 0.00  0.68  0.40  -0.64 -0.36 0.93
</shift>
Since my system is 12 bp long, it should have 11 inter base pair step values. But from the above information I am not sure which bp step is missing. Is there a way to identify this?
when I look at the file, cf_7methods.par, I see the above shift values are the same as given under the title "Curves base-pair step parameters".
Does this mean these values are calulated by curves? Can I extract the bp steps from this file?

thanks again,
Shyno

6

MD simulations / Re: issues with x3dna_ensemble

« on: June 03, 2013, 06:11:51 pm »

Hello Xianjun,
Thanks so much for your detailed message. This is very helpful. I have few more questions.
1. I am attaching the bpfile.dat, I notice the methylated cytosine (M) is recognized as just C. Is there a way to change this. Should I modify any of the files in x3dna-v2.1beta/
For example, some time back, I have included a line in baselist.dat
M C
Also I was using curves+ to do the analysis. The output of curves+, file named 'sel.lis' will keep the residue name as M.
I assume this doesn't make any difference to the values for the step parameters
2. For step parameters, the values listed in ensemble.out are taken from bp_step.par, correct?
Because I would like to extract the base pair steps along with the values. I didn't find the base pairs listed explicitly in the ensemble.out
When some of the bp steps are missing, it is confusing which value is associated with a particular bp step.
3. Also what is the difference between major_gw_pp and major_gw_refined and similar file for minor groove as well. I am interested in extracting the minor and major groove widths.
Please see the attached files.

thanks again,
Shyno

7

MD simulations / Re: issues with x3dna_ensemble

« on: June 03, 2013, 11:39:33 am »

Hello Xianjun,
I was able to install the ruby.. I am trying to understand the example. It would be great if you could answer the following questions:
1. When I run the command "find_pair sample_md0.pdb bpfile.dat", the output file bpfile.dat is different from the one given initially. For example, this file has 13 base pairs as opposed to 12 base pairs in the initial file.I noticed you said this is ok in your post wich I referred in the first message.
2. I am assuming the sample_md0.pdb is generated from the initial frame of the trajectory. For example, I have a trajectory consisting of 5000 frames and I am analysing all frames except the first 999 frames. So in this case, the file equivalent to sample_md0.pdb, will be the pdb file  corresponding to 1000 frame.
3. Now for the next step,
x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble.out
All the model_*.pdb files in the pdbdir are pdb files created for different frames (or timesteps)?
I am assuming this step works for just one frame also. Since my system contains water, and other ions, and I am writing a pdb file for each frame just selecting the dna alone.

thanks in advance for your help,

best
Shyno

8

MD simulations / Re: issues with x3dna_ensemble

« on: June 03, 2013, 10:19:41 am »

Hello Xianjun,
thanks so much for your reply. You are right, I don't have ruby installed in my system. I am trying to install it, but is running into some issues.

thanks
Shyno

9

MD simulations / issues with x3dna_ensemble

« on: May 30, 2013, 10:48:32 am »

Hi  all,,
I need some help. I am trying to use x3dna_ensemble to calculate the inter-base step parameters. I am trying to follow the steps mentioned by Xiang-Jun in the following post: http://forum.x3dna.org/md-simulations/how-to-properly-use-x3dna_ensemble/
this is what I did so far
1. I went inside the directory,
     X3DNA/x3dna-v2.1beta/examples/ensemble/md
2. Issued the command
     x3dna_ensemble analyze -h
but it is giving me the following message:
/usr/bin/env: ruby: No such file or directory
I also tried typing:
~/X3DNA/x3dna-v2.1beta/bin/x3dna_ensemble analyze -h
still got same message

In my .bashrc file, I have included the following two lines when I first installed (few months ago) x3DNA
export X3DNA=/home/shyno/X3DNA/x3dna-v2.1beta
export PATH=$PATH:$X3DNA/bin

thanks,
Shyno

10

MD simulations / Re: analyzing longer DNA sequences

« on: November 20, 2012, 05:58:55 pm »

thanks again for your detailed message.
I am not sure if this is too much to ask you.
But if you feed the output of find_pair , curves.inp to Curves+ as shown below
/Curves/cur+ < curves.inp
The output file (sel.lis) says
Strands =    2 Atoms =   978 Units =    48
which is correct as I need to analyze only 24BP. But the next line,
Combined strands have   15 levels ...

  Strand  1 has  15 bases (5'-3'): GTGTGAGCGTGGGCG
  Strand  2 has  15 bases (3'-5'): CACACTCGCACCCGC

doesn't seem correct as I would expect ~24 levels or (22-23 atleast). For Curves+ the maximumnumber of nucleotides it can analyze is 1000.

thanks
Shyno

11

MD simulations / Re: analyzing longer DNA sequences

« on: November 20, 2012, 03:13:06 pm »

Hi Xian- Jung,

thanks for your quick response.
Please see the attached files- this is for 27BP long double stranded DNA
Folllowing are the commands I use:
find_pair -c+ sel. pdb curves.inp
~/Curves/cur+ < curves.inp
I am attaching sel.pdb, curves.inp and the output of curves+ - sel.lis
for Curves, the maximum number of nucleotides we can have is '1000' and mine is well below.
So I thought the issue might be with find_pair

thanks
Shyno

12

MD simulations / analyzing longer DNA sequences

« on: November 20, 2012, 02:01:37 pm »

Hi all,

I am having difficulties analyzing a 62 base pair long DNA.I am using find_pair along with Curves+.
The 3DNA version I use -x3dna-v2.1beta
What is the default number of base pairs find_pair can analyze? Is there a way to increase this value?

Thanks
Shyno

13

MD simulations / Re: pdb files created using v 1.5 and v 2.1 beta

« on: May 29, 2012, 06:20:34 pm »

To be more clear about my previous question, I used the 'diff' command to see if these structures are different.
But when I loaded both structures in vmd, they looked the same.
thanks
Shyno

14

MD simulations / pdb files created using v 1.5 and v 2.1 beta

« on: May 29, 2012, 06:12:12 pm »

Dear users,

Initially I was using X3DNA v 1.5 for creating a pdb file, which I used for studying mutations.
Only recently I realized there are new versions of X3DNA and I tried creating the same pdb file using v 2.1 beta.
These two files seems to be different. Can anyone comment on this? does it mean the pdb file I created using v1.5 is not good?

Thank you very much,
Shyno Mathew

15

MD simulations / Re: No matching entry in atomlist.dat

« on: May 02, 2012, 01:42:02 pm »

Hello Xiangjun,

thank you very much for your reply.
You are correct, I don't need to modify the baselist.dat, actually I got that message with v 1.5 which I tried first. Now I am using v2.1beta.
Regarding the "No matching entry in atomlist.dat", my pdb format was wrong! Once I fixed that issue, everything seems fine.
thanks again for your reply and sorry for the delay in replying.

Regards
Shyno

16

MD simulations / No matching entry in atomlist.dat

« on: April 29, 2012, 07:49:24 pm »

Dear all,

I am trying to use find_pair as shown below:
find_pair -c+ sel.pdb new.inp
I am getting this error: no matching entry for atom name [  OW] (..OW) in 'atomlist.dat'
   now it is set as 'XX'
In my pdb file water is listed as OW. In this case should I add this as a new atom to atomlist.dat?
For the same analysis, I had to modify baselist.dat. The following bases were added:
DG3- 3 terminal guanine
DC5- 5 terminal cytosine

thanks
Shyno