Once you trajin the correct trajectory file, the general command for
calculating the distance between two atoms should be something like this:
distance DIST .atom_number1 .atom_number2 out dist.out
Or for your specific case, it should be:
distance DIST .256 .399 out dist.out
You could also use the residues numbers and atom types:
distance DIST :154.OE1 :45.OD2
Either of these last two commands should give you the exact same results for
your system.
Good luck!
-Bill Miller
On Mon, Mar 22, 2010 at 8:24 AM, imtiaz shafiq <imtiazshafiq.gmail.com>wrote:
> Dear All,
>
> I want to calculate a distance between two atoms vs time. Let us say I
> have two atoms with number 256 and 399 and the corresponding residue
> names are GLU 154 and ASP 45, The atom label are OE1 and 0D2, what
> could be the best option to calculate distance between these two
> versus the time.
>
> I have look at the Amber tools manual and found there is distance
> command available with ptraj but I am not sure what syntax I should
> use in my case. Please suggest me something in this regards
>
> Imtiaz
>
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Received on Mon Mar 22 2010 - 06:00:10 PDT
