AMBER Archive (2000)

Subject: RE: Restraints in Amber6

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Fri Nov 03 2000 - 13:33:45 CST


Thanks for the suggestion Bill, but unfortunately, the same "error" appears.

Troy

-----Original Message-----
From: Bill Ross [mailto:ross_at_cgl.ucsf.EDU]
Sent: Friday, November 03, 2000 9:27 AM
To: tbothwe1_at_bigred.unl.edu
Subject: Re: Restraints in Amber6

Try deleting the 2nd &end line.

Bill Ross
        --------------------------------------------------------------
        
         &cntrl
                imin=1,
                ncyc=50, maxcyc=1000,
                ntc=2, tol=0.000001,
                cut=9.0,
                ntpr=100,
                ntb=1,
                ntr=1,
         &end
                Group input for restrained atoms
                 100.00
                RES 1 28
         &end
                END
                END
        --------------------------------------------------------------------
        
        Here is the end of the output file where the "error" occurs:
        
        --------------------------------------------------------------------
                 5. REFERENCE ATOM COORDINATES
        
        
            ----- READING GROUP 1; TITLE:
                Group input for restrained atoms
        
             GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000
         GRP 1 RES 1 TO 28
              Number of atoms in this group = 889
            ----- READING GROUP 2; TITLE:
        
        
             rfree: End of file on unit 5
        --------------------------------------------------------------------
        
        The output file stops at that point. The command line I am using is:
        
        --------------------------------------------------------------------
        
        sander -O -i inputfile -c input.crd -p input.top -o outputfile -ref
        input.crd -r output.xyz &
        
        -------------------------------------------------------------------
        
        I was wondering if the error was the result of having the input.crd file
        also being the -ref file for the constraint? However, it seem to be
        restraining "group 1", but tries to restrain another group? I'm not sure
        what's going on.
        
        Thanks for your input and time!!!!
        
        Troy Bothwell