AMBER Archive (2009)

Subject: Re: [AMBER] NMR restraint

From: Sally Pias (sallypias_at_gmail.com)
Date: Tue Oct 27 2009 - 23:32:33 CDT

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_at_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
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber