Messages

1

MD simulations / Re: H-bonding information in MD analysis output

« on: October 04, 2011, 12:41:55 am »

Dear Xian-jun,

Thankyou for your help, I will try to work with the extract output and organise the data as you suggested. I guess I'm trying to make it easier to see the type of H-bond events that are occuring.

I am not experienced in programing/scripting so it will be an interesting challenge. I'll post the script here if I'm successful as others may have a use for it.

Much appreciated,

Andre

2

MD simulations / Re: H-bonding information in MD analysis output

« on: October 03, 2011, 05:19:29 pm »

Dear Xian-jun,

Ok, essentially I'm trying to group the H-bond information. Yes, there may be a lot of H-bond possibilities in a DNA structure including hoogsteen and reverse waston crick pairing.

This may be a process that the extract script will have to handle after 'analyze'.

Let's use wastson crick pairing as our conventional H-bond information. For your GC pair example, can we extract and organsie the information so the first column is O2 - N2, second is N3 - N1, and the third is N4 - O6. If there are non-waston crick H-bonds they can be placed in the fourth and subsequent columns.

Do we have to specify all the non-waston crick H-bonds or can the script look for the waston crick H-bonds and place the non-waston crick H-bonds after the standard waston crick information?

Here is a file of common H-bonding atoms between bases:

3

MD simulations / Re: H-bonding information in MD analysis output

« on: October 01, 2011, 11:16:58 pm »

Dear Xian-jun,

Thankyou for that, it works fine and it's exactly what I wanted. Since the H-bond information for each base pair is arranged in columns, is there a way for the script to define each column for a specific H-bond and if the bond does not exist then it will leave it blank?
Also if other 'non-standard' H-bonds form (shown by the asterisk ' * '), is it possible for the script to put these in seperate columns?

Here is a file to show you what I mean;

I realise this is just formatting however it will make life easier to have the script format the output rather than do it manually.

Kind regards,

Andre

4

MD simulations / Re: H-bonding information in MD analysis output

« on: September 29, 2011, 07:43:33 am »

Dear Xiang-Jun,

Thankyou very much for that. Greatly appreciated.

Kind regards,

Andre

5

MD simulations / Re: H-bonding information in MD analysis output

« on: September 29, 2011, 05:07:19 am »

Dear Xiang-Jun,

Thankyou for the quick reply.

Yes, I would like to have a new section with the H-bonding information in the output file, I am not familiar with ruby, and do not know how to do this using the x3DNA_md.rb script. There are 100 md*.out files to process for a given structure and the script has been very helpful in collecting the DNA parameters.

Kind regards,

Andre

6

MD simulations / H-bonding information in MD analysis output

« on: September 28, 2011, 12:35:23 am »

Hi All,

I have used the x3dna_md.rb script and it has worked perfectly. However, is there a H-bond parameter that it will analyse? I cannot see any H-bond information in the x3dna_md.out file.

Kind regards,

Andre