Hello Yao,
I think in AMBER, people use mask to achieve this goal.
Please see amber manual appendix C. ambmask .
Yun
On Fri, Oct 7, 2011 at 5:13 PM, Yao Yao <yao0o.ymail.com> wrote:
>
>
>
> ----- Forwarded Message -----
> From: Yao Yao <yao0o.ymail.com>
> To: Jason Swails <jason.swails.gmail.com>
> Sent: Friday, October 7, 2011 5:12 PM
> Subject: Re: [AMBER] Gromacs Make Index in AMBER
>
>
> make_ndx can choose specific atoms, groups or residues and make an index
> file for them,
> when calculating the energy or analyze the trajectory (rms, correlation,
> hbond ....), it can only calculate the properties of the indexed part alone
> if you include the index file when issuing commands.
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: Yao Yao <yao0o.ymail.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Friday, October 7, 2011 5:00 PM
> Subject: Re: [AMBER] Gromacs Make Index in AMBER
>
>
> Unlikely. What does make_ndx do exactly?
>
>
> On Fri, Oct 7, 2011 at 6:56 PM, Yao Yao <yao0o.ymail.com> wrote:
>
> Hi,
> >
> >In gromacs I often use make_ndx command to pick specific atoms, groups or
> residues of my interest
> >for energy calculation purpose or so on. Does AMBER has similar command or
> flag I can use?
> >
> >Thanks,
> >
> >Yao
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sat Oct 08 2011 - 09:00:04 PDT
