AMBER Archive (2006)

Subject: Re: AMBER: Ptraj selecting specific atoms in specific residues

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Wed Aug 16 2006 - 12:19:31 CDT


Steve,

Have you tried using your first command without a space between ':1-2' and
'@CA,N'?

Scott

On 8/16/06, Steve Seibold <seibold_at_chemistry.msu.edu> wrote:
>
> Hello
>
> I hope I am not missing something simple, but I do have a simple question
> concerning the use of "ptraj". I am trying to get rms and atomicfluc values
> for specific "atoms" in specific "residues". For example, let say I have a
> protein that is 200 residues and I want to find the rms of CA of only the
> first two residues. I tried the following:
>
>
>
> *rms mass out file.txt time 5 :1-2 @CA,N*
>
>
>
> *atomicfluc out file.txt @CA,N :1-2*
>
> * *
>
> Neither of these commands seems to work. I do get data but it is NOT the
> data I am searching for. In the first case I get all atoms of residues 1 and
> 2. In the second case I get atoms CA and N of the whole protein.
>
>
>
> Am I doing something wrong or does AMBER not do this?
>
>
>
> Thanks, Steve
>
>
>

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