AMBER Archive (2006)

Subject: AMBER: MD with positional and NMR restraints

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Thu Dec 07 2006 - 14:46:26 CST

I can use the following two sripts to do MD simulations (A) with
atoms held at fixed positions, or (B) with atoms restrained by NOE
restraints.

Is there any way to use both positional and NOE restraints? The script
shown in (C) below runs but does not implement the NOE restraints.

Thanks,

Mike

(A) #########################################
 &cntrl
    imin=0,
    irest=0,
    ntx=1,
    ntb=0,
    cut=10,
    ntc=2,
    ntf=2,
    tempi=0.0,
    temp0=300.0,
    ntt=3,
    gamma_ln=1.0,
    nstlim=10000, dt=0.002,
    ntpr=100, ntwx=100, ntwr=1000
    ntr=1,
/
 keep main chain atoms frozen
 500.0
FIND
* * M *
SEARCH
RES 1 145
END
END
eof

sander -O -i md-nmr.in -o md-fix.2.out -c ../min-vac/ca-min.rst -p ../ca.top \
-r md-fix.2.rst -x md-fix.2.trj -ref ../min-vac/ca-min.rst

(B) ############################################################
 &cntrl
    nmropt=1,
    imin=0,
    irest=0,
    ntx=1,
    ntb=0,
    cut=10,
    ntc=2,
    ntf=2,
    tempi=0.0,
    temp0=300.0,
    ntt=3,
    gamma_ln=1.0,
    nstlim=10000, dt=0.002,
    ntpr=100, ntwx=100, ntwr=1000
    ntr=0,
/

 &wt type='END' /
LISTOUT=POUT
DISANG=../RST.dist
eof

sander -O -i md-nmr.in -o md-nmr.out -c ../min-vac/ca-min.rst -p ../ca.top \
-r md-nmr.rst -x md-nmr.trj

(C) (Doesn't apply the NMR restraints.. permutations I've tried also don't work) ############

 &cntrl
    nmropt=1,
    imin=0,
    irest=0,
    ntx=1,
    ntb=0,
    cut=10,
    ntc=2,
    ntf=2,
    tempi=0.0,
    temp0=300.0,
    ntt=3,
    gamma_ln=1.0,
    nstlim=10000, dt=0.002,
    ntpr=100, ntwx=100, ntwr=1000
    ntr=1,
/

 &wt type='END' /
 keep main chain atoms frozen
 500.0
FIND
* * M *
SEARCH
RES 20 145
END
END

 &wt type='END' /
LISTOUT=POUT
DISANG=../RST.dist
/
eof

sander -O -i md-nmr-fix.in -o md-nmr-fix.out -c ../min-vac/ca-min.rst -p ../ca.top \
-r md-nmr-fix.rst -x md-nmr-fix.trj -ref ../min-vac/ca-min.rst

#################################################################################

When I execute (C), the output file includes the following:

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
                         ** No weight changes given **

 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

 Number of triangulated 3-point waters found: 0

     Sum of charges from parm topology file = -3.00000005

Thanks,

Mike 

-- 

*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle 
Baltimore, MD 21250

Phone: (410)-455-2527  
FAX:   (410)-455-1174
Email: summers_at_hhmi.umbc.edu
Web:   www.hhmi.umbc.edu
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