AMBER Archive (2004)

Subject: Re[4]: AMBER: rmsd over residues using ptraj

From: Qiang Lu (
Date: Wed May 19 2004 - 14:19:33 CDT

Hi Bill,

    Thanks for your help. I finished it. The input of carnal is as the following:

FILES_IN PARM p1 1tsr_b_ww_nc_nd_lb_sa_5.parm7;
STREAM s1 1tsr_b_ww_nc_nd_lb_sa_5.10ns.crd;
STATIC ref_set 1tsr_b_ww_nc_nd_lb_sa_5.00.rst;
TABLE tb1 sm1.rms;
TABLE tb2 sm2.rms;
TABLE tb3 sm3.rms;
TABLE tb4 sm4.rms;
TABLE tb5 sm5.rms;
GROUP grp ((ATOM NAME CA C O N)&(RES 1-194)); RMS fit FIT grp s1 ref_set;
GROUP g1 ((RES 1)&(ATOM NAME CA C O N)); RMS fit1 g1 fit;
GROUP g2 ((RES 2)&(ATOM NAME CA C O N)); RMS fit2 g2 fit;
GROUP g3 ((RES 3)&(ATOM NAME CA C O N)); RMS fit3 g3 fit;
GROUP g4 ((RES 4)&(ATOM NAME CA C O N)); RMS fit4 g4 fit;
GROUP g5 ((RES 5)&(ATOM NAME CA C O N)); RMS fit5 g5 fit;
TABLE tb1 fit1;
TABLE tb2 fit2;
TABLE tb3 fit3;
TABLE tb4 fit4;
TABLE tb5 fit5;

Best regards,

=================Original message text=============== > That will align the proteins only based on the marked residue > but not the whole protein. That will cause error.

The carnal version allows simply "rmsid%residues" to get the per-residue rms in a table, where the protein can be positioned to fit to any subset of atoms in the reference frame including (default) all atoms.

Bill -----------------------------------------------------------------------

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