# Re: [AMBER] Problem regarding RMSD

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Sat, 2 Feb 2019 04:46:21 +0000 (UTC)

Yes, sir. I wanted to calculate the rmsd different atoms containing residues.

Thanks and Regards,
Saikat Pal

On Saturday, 2 February, 2019, 2:18:57 am IST, Daniel Roe <daniel.r.roe.gmail.com> wrote:

Just for future reference, I think your problem was that you had

:11.N1,C2,O2,N3,N4,C5,C6,12.N1,C2,N3,C4,C5,C6,C7,O4,O2

when you wanted

:11.N1,C2,O2,N3,N4,C5,C6,12 .N1,C2,N3,C4,C5,C6,C7,O4,O2

Or was it something else?

-Dan

On Thu, Jan 31, 2019 at 9:50 AM Saikat Pal <saikatpaliitg.yahoo.com> wrote:
>
>  Dear all,I want to perform rmsd of the certain residue for my case resid 11 and 12. But the problem is that the residue 11 and 12 are cytosine and thymine respectively.So I have considered the heavy atoms of the residues for cytosine N1,C2,O2,N3,N4,C5,C6 atoms and for thymine  N1,C2,N3,C4,C5,C6,C7,O4,O2 atoms.The total number of the atom is 16.
> I have used this command to calculate the rmsd:
> rmsd loop-3 :11.N1,C2,O2,N3,N4,C5,C6,12.N1,C2,N3,C4,C5,C6,C7,O4,O2 ref [inp] out rmsd-loop-3.dat mass
> But when I have run the command using cpptraj it considers the huge number of atoms (1388):
> 8: [rmsd loop-3 :11.N1,C2,O2,N3,N4,C5,C6,12.N1,C2,N3,C4,C5,C6,C7,O4,O2 ref [inp] out rmsd-loop-3.dat mass]
>
>
>
> Thanks and Regards,
> Saikat Pal
>
>
>
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Received on Fri Feb 01 2019 - 21:00:01 PST
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