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
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Received on Thu May 12 2011 - 16:30:04 PDT
