AMBER Archive (2005)

Subject: Re: AMBER: RMSD Calculations

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Mon Dec 05 2005 - 10:56:36 CST

the strip command will do that, and that will work fine as long as
you have a prmtop without the extra residue. something like this:

1) run ptraj with prmtop that has teh extra residue

trajin trajfile.x
trajout newtrajfile.x nobox
strip :residuename

2) re-run ptraj with new traj file
trajin newtrajfile.x
reference crdfilename
rms reference out rmsfilename :yourmask

carlos

Kara Wald wrote:

> Do you know of a way to remove a residue from every frame of a
> trajectory? I guess I could do that as my analogs are the last
> residue in the list. If I could do this, I would be left with only
> the DNA which would have the same number of atoms.
>
> Kara Di Giorgio
>
>
> On Dec 5, 2005, at 8:00 AM, Carlos Simmerling wrote:
>
>> for ptraj you do indeed need to have the same number of atoms
>> in the reference structure as you have in the prmtop that you load
>> into ptraj.
>> if you can get that resolved then the other issues would be ok.
>>
>> Kara Di Giorgio wrote:
>>
>>
>>>
>>>
>>> I'm also worried that it will only calculate the RMSD if there are
>>> an identical number of atoms in each, which I don't have.
>>>
>>>
>>
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