Hi,
You can use the new loop and script variable functionality in cpptraj
(you need an up-to-date version, either from GitHub or Amber18).
For example:
for i=1;i<10;i++
for j=2;j<10;j++
distance d_$i_$j out dist.dat
done
done
Or something like:
for atoms A0 inmask :1-10 i=1;i++
distance d$i :11 $A0 out dist.dat
done
See the manual for more details, in particular look at the new 'for'
and 'set' commands (section 29.3 Variables and Control Structures).
You can also use pytraj as Wesley suggested.
-Dan
On Tue, Jun 5, 2018 at 12:53 PM, 唐元晖 <tangyuanhui08.126.com> wrote:
> Hello all,
>
>
> This is Yuanhui. I want to calculate the distance between two residues as :i and :j, and i, j can be changed during a loop. However, the distance mask doesn't recognize the word :i. The input file is written like this:
>
>
> parm *.prmtop
> trajin md15.mdcrd 1 last 200
> i=2
> j=3
> distance dist :i :j out dist.dat
>
>
> Is there a way can make the cpptraj recognize the variable 'i' and 'j', because I want to change their values.
> Best wishes!
>
>
>
> --
>
> Dr. Yuanhui Tang
> Ralph E. Martin Department of Chemical Engineering
> University of Arkansas
> Cato Springs Research Center
> Fayetteville, AR 72701
> email: yt006.uark.edu
> voice: (479) 409-9989
>
>
>
>
>
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Received on Tue Jun 05 2018 - 12:30:03 PDT
