On Fri, May 13, 2011 at 1:48 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Hi Devlina
>
> You are defining ntr=1 but not defining restraint_wt and retsraintmask.
>
Good catch. This is the issue. The error is occurring in subroutine rfree,
which is where the group input is read (which is only used if you don't
define restraintmask and restraint_wt).
Thanks Sangita,
Jason
>
> > The error message is this:
> >
> > rfree: End of file on unit 5
> >
> > which means that it probably couldn't find the &cntrl namelist, or it
> > couldn't find the end of it. Here are 2 things to try:
> >
> > Put a space before the first character of every line, including &cntrl
> and
> > &end. Use the character "/" to terminate the namelist instead of "&end".
> >
> > Some compilers are strangely picky here. If either of these two
> suggestions
> > DO work, could you post your system specs (system architecture and
> > compilers) just so I can keep in mind what kind of systems this is an
> issue
> > for?
> >
> > Thanks!
> > Jason
> >
> > On Thu, May 12, 2011 at 2:13 PM, Devlina Chakravarty <
> > devlina.chakravarty.gmail.com> wrote:
> >
> >> Hi! I was trying to run a short md run on a domain of tubulin bound
> >> with a ligand, using GB model to represent solvation effects. The part
> >> till minimisation went fine, then I went on to equilibrate the
> >> minimised structure using a file which contains the following lines,
> >>
> >> # equilibrate structure #
> >> &cntrl
> >> imin=0
> >> ntc=2, ntf=2,
> >> cut=12.0, igb=1, saltcon=0.2, gbsa=1
> >> ntpr=10,
> >> nstlim = 5000, dt=0.002
> >> ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
> >> ntx=1,irest=0, ntb=0,
> >> nscm = 1000,
> >> ntr=1,
> >> &end
> >>
> >> The job is given as : sander -O -i equil.in -c 1sa0.rst -p
> >> 1sa0.top -ref 1sa0.rst -o 1sa0.equil.out -r 1sa0.equil.rst
> >>
> >> However, the run is not completed and it ends abruptly without
> >> generation the1sa0.equil.rst file , I have included the file which it
> >> generates. Please could you help me out with this.
> >>
> >> --
> >> Devlina Chakravarty
> >> JRF
> >> Bose Institute
> >> Kolkata
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 13 2011 - 09:30:03 PDT
