Messages

1

General discussions (Q&As) / Re: generating 10.5 bp/turn B-DNA

« on: November 11, 2013, 11:25:44 am »

Dear Xiang

Thanks for the support. Regarding AMBER usage and for the benefit of new AMBER users I provide here link (AMBER tutorial) for simulating small fragment of DNA that includes minimization procedure as well

http://ambermd.org/tutorials/basic/tutorial1/

Most of the times more or less this (above link) protocol works with normal DNA.

kind regards
Jiomm

2

General discussions (Q&As) / Re: generating 10.5 bp/turn B-DNA

« on: November 11, 2013, 09:27:48 am »

Dear Xiang

Thanks a lot for reply.

>> I do not understand your rationale of changing rise from 3.37 Å to 3.5385

Sorry, I was in wrong impression that with change in base pair per turn (in my case 10 to 10.5) the overall length should also change. But its wrong, overall length should not change and thus rise should be same.

Also regarding PHENIX, I never used that before. Actually I need to use this rebuilt structure for AMBER simulations so before molecular dynamics I will perform minimization with AMBER which should take care of geometric concerns. Do you still think that I should use PHENIX before AMBER minimization?

kind regards
Jiomm

3

General discussions (Q&As) / generating 10.5 bp/turn B-DNA

« on: November 10, 2013, 03:55:16 pm »

Dear Xiang

{Sorry, I posted personal mail earlier. Now I am using "New Topic", hope it goes to all}

I explored your online tools and found them  very useful. For Fibre BDNA generic form we can get 36 degree twist and 3.37 rise as default values. I have B-DNA sequence pdb (MY.pdb; also your tool can help to generate directly 10 bp B-DNA) with 10 bp/turn and want same B-DNA sequence as 10.5 bp/turn. Please let me know if following process would be correct to generate 10.5 bp B-DNA:

1) Analyse this MY.pdb (having 10bp/turn) using Analysis tool online.

2) Save the Nucleic Acid Local Base Step Parameters and Local Base-pair Parameters and write on text file. Edit the text file and modify each twist to 34.29 keep rise same as 3.54  (which is obtained as: twist= 360/10.5; and rise = 3.37+ (3.37/2)/10 = 3.5385 ). I am not sure about the rise especially and others. Should I keep other params same?

3) Generate new B-DNA with using this edited parameter file (Reconstruction--> customised model)

Please let me know if this procedure is correct?

kind regards
Jiomm