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

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Wed, 19 May 2004 14:15:01 -0700 (PDT)

Hi Qiang,

> The input of carnal is as the following:
        
        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
        
You could put all the data in 1 table if you wanted - e.g.
"TABLE tb1 fit1 fit2 fit3 fit4 fit5;"

The way to get global rms followed by rms for each residue into
one file would be "TABLE tb1 fit fit%residues;"

Bill
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Received on Wed May 19 2004 - 22:53:00 PDT
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