Re: [AMBER] Fw: Gromacs Make Index in AMBER

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 8 Oct 2011 12:59:41 -0400

You still can't get energies based on mask selections as far as I know. Other properties are possible through ptraj and cpptraj on a per-mask basis

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Oct 8, 2011, at 11:58 AM, Yun Shi <yunshi09.gmail.com> wrote:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> 
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Received on Sat Oct 08 2011 - 10:30:02 PDT