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.hhmi.umbc.edu
Web: www.hhmi.umbc.edu
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Received on Fri Dec 08 2006 - 16:23:19 PST
