AMBER Archive (2000)

Subject: Restraints in Amber6

From: Troy Bothwell (tbothwe1_at_bigred.unl.edu)
Date: Fri Nov 03 2000 - 12:35:31 CST

Amber users,

I could really use some help in tracking down a problem I'm having with
restraining my solute (14mer DNA oligo) while allowing the solvent (H2O and
counter ions) to relax.

Here is my input file:

--------------------------------------------------------------

 &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