AMBER Archive (2009)

Subject: [AMBER] NMR restraint

From: xuemeiwang1103 (xuemeiwang1103_at_163.com)
Date: Tue Oct 27 2009 - 21:31:39 CDT

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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