[AMBER] RMSD on two slightly different structures

From: Guillaume Roellinger <roellinger.bio.mx>
Date: Mon, 22 Sep 2014 07:18:47 +0000

Dear all,

Using cpptraj, I am computing the RMSD between two almost similar structures with two different topology files and then perform a PCA. Structure A has 265 residues and structure B: 271. The sequence in structure A from residue 1 to 265 is the almost the same (there are 2-3 mutations) as in structure B from residue 5 to 270.

I am computing the RMSD this way and it is working:

parm structureA.prmtop
parm structure B.prmtop
trajin structureA.pdb parmindex 0
trajin structureB.pdb parmindex 1
reference structureA.pdb parmindex 0
rms reference :1-265.CA

1st question: When I am selecting the residue range 1-265, does it take from both structure A and B the residues 1 to 265 or does it select from structure A residues 1 to 265 and from structure B residues 5 to 270 (=the almost common sequence part)?

2nd question (related to the first one): In an other example, I have structures C with 278 residues and D with 277. What appends if I have "gaps" in both sequences and if I compute the RMSD with :1-277.CA as mask (this is working as well!) ?

Thanks in advance for your answer,


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Received on Mon Sep 22 2014 - 00:30:02 PDT
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