AMBER Archive (2005)

Subject: Re: AMBER: RMSD Calculations

From: Kara Wald (kdigiorgio_at_sbcglobal.net)
Date: Mon Dec 05 2005 - 10:39:44 CST

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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