Messages

1

MD simulations / Re: 3DNA changes base-pair order

« on: April 21, 2015, 11:16:26 am »

Dear Xiang,
Thank you very much for your update. and sorry for my late late reply.
I have tried the new version and it seems that it works for me!
This will be a great help for those who carry out MD simulations.
Best
Arman

2

MD simulations / Re: 3DNA changes base-pair order

« on: March 19, 2015, 05:32:38 pm »

Dear Xiang,
Thanks very much indeed.
I really appreciate it.
Just want to make a suggestion which I think might be helpful for MD analysis in general. It would be better if 3DNA had the option of skipping those pdb input files presented in the pdb_list and just gave a warning that for example this pdb contains distorted base-pairs and then resumed analysis of the rest of the files. Otherwise, one needs to  run it and checked any time for all the distorted files in a trajectory.

Thank you very much again and with the best regards
Arman

3

MD simulations / Re: 3DNA changes base-pair order

« on: March 16, 2015, 06:50:02 pm »

Thanks.
Here I have attached three pdb files that I am using them for analysis. the first and last one can be analyzed without any problems. But if you add them in a pdb_list file, when it starts to analyze frame1067.pdb the error message pops out. I also attached the inp.inp file which is the template for base-pairs generated by find_pair command.
I found that when I use find_pair for frame1067.pdb even with the modified variables of misc_3DNA.par, still it does not recognize one of the base-pairs so that could be the source of error. But I do not know what else could I do to resolve it.

Regards

4

MD simulations / Re: 3DNA changes base-pair order

« on: March 16, 2015, 06:26:58 pm »

Dear Xiang,
Thank you so much.
The problem is that when I use a sane input file, generated by find-pair and use it as a template for x3dna_ensemble, at a snapshot I get this error and process stops:
Error in running command: '/mnt/store2/home/.../bin/analyze -c  temp_model.inp 2> msgfile'
Rerun the command w/o redirection for details

this is the command that I used:
x3dna_ensemble analyze -b inp.inp -l pdb_list.txt -o ensemble.out

and I have changed values in the misc_3DNA.par file to avoid former unknown base-pairs problems.
Can you please also help me with that?
I really appreciate it.
Best

5

MD simulations / Re: 3DNA changes base-pair order

« on: March 16, 2015, 02:40:50 pm »

Dear Xiang,
Thanks very much indeed for your comprehensive and prompt reply.
The command analyze -c was very helpful and one of my problems just solved.
Also thank you for sending me the links. I am already familiar with MD analysis of 3DNA and I just posted the two snapshots to clear my point.

But still my biggest concern remains that the order of base-pairs or maybe name of them is changing in different snapshots. For example base-pair 169 in '29999.par' is C-G but in '30000.par' is G-C. Do you know why that happens? If they were in a goos order, at least I could find out which base-pair is highly deformed that cannot be understood by 3DNA.

Thank you very much again
Arman

6

MD simulations / 3DNA changes base-pair order

« on: March 16, 2015, 12:04:09 pm »

Dear All,
I am trying to use 3DNA to extract step parameters of a circular DNA from a MD simulation of 180 base-pairs.
I use find-pair and analyze commands to get cf_7methods file. Here I have attached 2 output files and the corresponding analysed files which only have 1 picoseconds in between but some problems occur:
1- in one of them number of recognized bse-pairs are less thatn the other.
2- For some base-pairs, the base-pair step parameters cannot be obtained and 3DNA gives "----". I tried to play with all parameters of the misc_3DNA.par but still there are some unknown parameters for some base-pairs.
It seems that for highly deformed bases or base-pairs 3DNA do not consider them as bases (base-pairs). Is there any way to ignore it?
3- Last but not the least, 3DNA changes order of base-pairs in the file. For example compare the sequence of base-pairs 160 to 180 in the files 29999.par and 30000.par . (the 30000.par is the correct sequence). Is this only a mistake in the written sequence or everything has been changed?

Thanks in advance
With the best regards
Arman