Sorry, my mistake, I omitted the [p_ref], seemed starnge to me ... now
it works to load into ccptraj. With ccptraj he does the tranlstion
correctly with:
rmsd reference .CA .CA out test.list out results
What is "[p_ref]", could not find it in the manual ... stupid question I
suppose.
Thanks again Dan!
On 05/09/2013 09:41 PM, Daniel Roe wrote:
> Hi,
>
> One of the strengths of cpptraj is that it allows you to specify
> multiple topologies, as well as different target and reference masks
> to the rms command - the only requirement is that the # of atoms and
> their ordering are the same. For example, the input may be something
> like (assuming :63-65.CA,C,N is your target mask and
> :94,146,220.CA,C,N is your reference mask):
>
> parm ref_structure.pdb [p_ref] # This loads ref_structure.pdb as a
> topology tagged [p_ref]
> reference ref_structure.pdb parm [p_ref] # This loads the coordinates
> from ref_structure.pdb as the reference
> trajin prorun_reimaged.mdcrd
> rms reference :63-65.CA,C,N :94,146,220.CA,C,N out results.dat
>
> On Thu, May 9, 2013 at 11:02 AM, Andre C. Stiel
> <andre.stiel.tuebingen.mpg.de> wrote:
>> 2) the rmsd results are absolutely bogus. It looks like in the first
>> step where I did NOT specified "nofit" he
>> did no fitting or he didnt translate the frame.... I always figured
>> ptraj would translate the frame if no "nofit" is specified
> No, in ptraj and cpptraj 'nofit' means straight RMSD, do not modify
> the coordinates in any way. In cpptraj you can get RMS results with
> translation and without rotation by specifying the 'norotate' keyword.
>
> Hope this helps,
>
> -Dan
>
>> In short: I want to first superimpose a set of relatively fixed atoms
>> and then measure the rmsd w/o fitting of my moving atoms.
>>
>> Maybe somebody can help me out.
>> Thanks a lot
>>
>> André
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 10 2013 - 06:00:06 PDT
