I do not know if this will help, but I suggest that you try the
slightly modified input below. I have simply added a comma ( , )
following the last statement in your &cntrl namelist and have replaced
all occurrences of &end with the " / " token. (You had both &end and
" / " at the end of your &rst namelist.) See Amber 9 manual page 293
for a discussion of namelist syntax.
Stage 1 heating of 1oop 0 to 50K
&cntrl
imin=0,irest=0,ntx=1,
nstlim=5000,dt=0.001,
ntc=2,ntf=2,
ntt=3,gamma_ln=1.0,
tempi=0.0,temp0=50.0,
ntb=1,cut=8,
ntr=1,nmropt=1,
ntpr=250,ntwx=500,ntwr=500,
/
&wt type='REST',istep1=1,istep2=5000,
value1=1.0,value2=1.0,
/
&wt type='END',
/
LISTOUT=RST.out
DISANG=dis.RST
------dis.RST------
#DISTANTENT.FILE
&rst
ixpk= 0, nxpk= 0, iat= 9292, 7786, r1= 1.20, r2= 1.50, r3= 2.00, r4=
5.00, rk2=10.0, rk3=10.0, ir6=1,
/
2009/10/27 xuemeiwang1103 <xuemeiwang1103.163.com>:
> Dear Dr. :
> Thanks for your previous help .This morning ,someone suggest me to use the distance restriant in the MD simulation , not in the minimal,so I tried it ,this time it seems work ,but still error ,I aologize for have wasting your time, your comments are highly appreciate! BTW,I use the Amber9 , Don't the NMR restraint work in the minnimal simulation?
> my input:
> Stage 1 heating of 1oop 0 to 50K
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=5000,dt=0.001,
> ntc=2,ntf=2,
> ntt=3,gamma_ln=1.0,
> tempi=0.0,temp0=50.0,
> ntb=1,cut=8,
> ntr=1,nmropt=1,
> ntpr=250,ntwx=500,ntwr=500
> /
> &wt type='REST',istep1=1,istep2=5000,
> value1=1.0,value2=1.0, &end
> &wt type='END', &end
> LISTOUT=RST.out
> DISANG=dis.RST
> ------dis.RST------
> #DISTANTENT.FILE
> &rst
> ixpk= 0, nxpk= 0, iat= 9292, 7786, r1= 1.20, r2= 1.50, r3= 2.00, r4= 5.00, rk2=10.0, rk3=10.0, ir6=1, /
> &end
> command: sander -O -i heat1.in -p 1oop.prmtop -c min.rst -o heat1.out -r heat1.rst -ref min.rst -x heat1.mdcrd &
> the error :
> forrtl: severe (24): end-of-file during read, unit 5, file /home/heat1.in
> Image PC Routine Line Source
> sander 084E1F3C Unknown Unknown Unknown
> sander 084E1A34 Unknown Unknown Unknown
> sander 084AED95 Unknown Unknown Unknown
> sander 08472648 Unknown Unknown Unknown
> sander 08472AEB Unknown Unknown Unknown
> sander 0848AD3C Unknown Unknown Unknown
> sander 08143D26 Unknown Unknown Unknown
> sander 080F54E1 Unknown Unknown Unknown
> sander 080D0AE1 Unknown Unknown Unknown
> sander 080CFB2D Unknown Unknown Unknown
> sander 0804A458 Unknown Unknown Unknown
> Unknown 00A18DE3 Unknown Unknown Unknown
> sander 0804A311 Unknown Unknown Unknown
> The output file :
> .......
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
> 5. REFERENCE ATOM COORDINATES
>
>
>
>
>
>
>
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>
>
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Received on Tue Oct 27 2009 - 22:00:03 PDT
