Re: [AMBER] Problem regarding RMSD

From: Daniel Roe <>
Date: Fri, 1 Feb 2019 15:48:30 -0500

Just for future reference, I think your problem was that you had
combined the target and reference masks, right? E.g. you had


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?


On Thu, Jan 31, 2019 at 9:50 AM Saikat Pal <> 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]
> Target mask: [:11.N1,C2,O2,N3,N4,C5,C6,12.N1,C2,N3,C4,C5,C6,C7,O4,O2](1388)
> Reference mask: [:11.N1,C2,O2,N3,N4,C5,C6,12.N1,C2,N3,C4,C5,C6,C7,O4,O2](1388)
> Thanks and Regards,
> Saikat Pal
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Fri Feb 01 2019 - 13:00:02 PST
Custom Search