Hi Devlina
You are defining ntr=1 but not defining restraint_wt and retsraintmask.
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Fri May 13 2011 - 05:00:03 PDT
