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;
FILES_OUT
TABLE tb1 sm1.rms;
TABLE tb2 sm2.rms;
TABLE tb3 sm3.rms;
TABLE tb4 sm4.rms;
TABLE tb5 sm5.rms;
DECLARE
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;
OUTPUT
TABLE tb1 fit1;
TABLE tb2 fit2;
TABLE tb3 fit3;
TABLE tb4 fit4;
TABLE tb5 fit5;
END
--
Best regards,
Qiang mailto:qiangl.uci.edu
=================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
-----------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed May 19 2004 - 20:53:00 PDT
