Thanks Trevor,
For your support
On Wed, Sep 22, 2010 at 1:01 PM, Trevor Gokey <tgokey.mail.sfsu.edu> wrote:
> Hirdesh: Yes my apologies... I actually meant to give the link I used at
> the end but it slipped my mind. It was the page I used heavily when I was
> new with ptraj. I use it as my "cheat-sheet" because a) it uses 95% of what
> I need in ptraj and b) it's the first thing to show up in a "ptraj tutorial"
> search via google. Very convenient.
>
> http://ambermd.org/tutorials/basic/tutorial5/
>
> Tangent to Ross: looking forward to your GTC talk.
>
> Trevor
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: Tuesday, September 21, 2010 10:46 PM
> To: 'AMBER Mailing List'
> Subject: Re: [AMBER] molecular dynamics simulation-water-box-diffution
> problem
>
> Hi Hirdesh,
>
> > I request to elaborate it a little bit more. It is ok for persons having
> > great hand with amber but for for beginners, it may be not so clear that
> how
> > to use these three lines.. what will be the input and what will be the
> > output. Please suggest the tutorial if you can.
>
> You cannot expect a tutorial for everything. The tutorials are designed to
> get you started but beyond that one is expected to actually seek to
> understand what is going on. They are encouraged to make you think
> independently and troubleshoot things for yourself. Such independent
> troubleshooting is a vital skill that you will need to master if you want
> to
> become a successful research scientist.
>
> I suggest looking at the AMBER Tools manual, specifically read the ptraj
> section. Each of the commands Trevor mentioned is clearly and concisely
> explained there along with syntax.
>
> If you have not already done so I would also suggest starting with Tutorial
> B1 here: http://ambermd.org/tutorials/ and then work progressively through
> each one in turn.
>
> Good luck,
> Ross
>
>
>
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>
--
Thanks and Regards,
Hirdesh,
******************************************
Hirdesh Kumar
PhD Scholar
School of Biological Sciences
Indian Institute of Technology, Delhi
Hauz Khaas, New Delhi-16
http://www.iitd.ac.in/bioschool.html
******************************************
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Received on Wed Sep 22 2010 - 03:00:07 PDT
