[AMBER] Problem regarding RMSD

From: Saikat Pal <saikatpaliitg.yahoo.com>
Date: Thu, 31 Jan 2019 14:50:03 +0000 (UTC)

 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

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Received on Thu Jan 31 2019 - 07:00:02 PST
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