AMBER Archive (2009)

Subject: Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj

From: workalemahu berhanu (wgberhanu_at_gmail.com)
Date: Mon Aug 17 2009 - 08:26:35 CDT

Dear Dr Ross
Hi
If you remember I asked you this same question at the summer workshop
at UCSD. Your advice was to post my question on the forum. May be the
way I put my question was not so clear. I have attached a graph that
shows the change in the number of total hydrogen bonds versus the
simulation time. I am interested in getting the raw data to make
similar plot from my trajectory file

With regards

Thank you

On Sun, Aug 16, 2009 at 8:30 PM, Ross Walker<ross_at_rosswalker.co.uk> wrote:
> See section 6 of tutorial B3 :
> http://ambermd.org/tutorials/basic/tutorial3/section6.htm
>
> It should be fairly easy for you to modify the donor / acceptor definitions
> for your system.
>
> Good luck,
> Ross
>
>> -----Original Message-----
>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of workalemahu berhanu
>> Sent: Sunday, August 16, 2009 1:13 PM
>> To: AMBER Mailing List
>> Subject: [AMBER] Variations of the number of total hydrogen bond in MD
>> simulations using ptraj
>>
>> Dear amber users
>> I would like to analysis my trajectory file for the change in the
>> total number of hydrogen bonds in my peptide and peptide with ligand
>> which is having beta sheet secondary structure in MD simulation. Is it
>> possible to do it using ptraj? Could anyone provide me a script for
>> this kind of analysis?
>> Thank you
>> With regards
>>
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