Thanks a lot Jason for your patient answer :)
On 08/30/2011 05:04 PM, Jason Swails wrote:
> On Tue, Aug 30, 2011 at 10:41 AM, Jan-Philip Gehrcke <
> jgehrcke.googlemail.com> wrote:
>
>> Hey.
>>
>> Using cpptraj, I am interested in how to get the RMSD of a certain
>> region within two structures after fitting these structures using
>> another region. The same question was already answered for ptraj:
>> http://archive.ambermd.org/201102/0128.html
>>
>> Quote by Dan:
>> "
>> reference refstruct.rst7
>> rms reference :1-100
>> rms reference :50-55 nofit out rmsd.dat
>>
>> The first rms command performs the best fit, then the second rms
>> command calculates the rmsd you want without changing the fit from the
>> first rms command.
>> "
>>
>> This is what I propose for cpptraj (for my system):
>>
>> parm topology.top
>> trajin traj1.mdcrd
>> rmsd :1-150 first
>>
>
> This aligns all structures by minimizing the RMS of that structure against
> the first structure using only residues 1-150 when calculating the RMS.
>
>
>> rmsd :151-161 first nofit out rmsd.dat
>>
>
> This calculates the RMS between each structure using residues 151-161
> *without* first doing a fit to that region. Thus, the structures will still
> be aligned according to the RMS command above (since that one is executed
> first).
>
>
>> Would that for each frame
>> 1) align the residues 1-150 of the current frame to the residues 1-150
>> of the first frame and then
>> 2) calculate the RMSD for residues 151 to 161 with the alignment from
>> (1) (again current frame vs. first frame)?
>>
>
> Yes.
>
> HTH,
> Jason
>
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Received on Wed Aug 31 2011 - 02:30:03 PDT
