On Thu, May 5, 2011 at 12:07 PM, siddesh southekal
<siddeshonline.gmail.com>wrote:
> Dear Users ,
>
> I am trying to run MD of a protein in a lipid environment to which a ligand
> molecule is docked using the AutoDock program . I did not have any problem
> when i ran MD of the protein in lipid environment without the ligand
> molecule .
> But i face problems once i dock the ligand molecule into the protein .
>
> After I minimize the system (ligand-protein complex) and then I try to run
> MD in the heating stage , the simulation runs without any problem ( but as
> long as the wall clock is given , which should end in much shorter time )
> and completes without any error in the .out file . The standard error file
> consists of the following error . Same error occurs even in
> water environment .The .rst file cannot be used again and the simulation
> gets aborted.
>
> forrtl: error (78): process killed (SIGTERM)
> forrtl: error (78): process killed (SIGTERM)
>
This tells me that the program received a termination signal. This is
either done by using CTRL-C in an interactive terminal, or it's sent by the
queuing system if you blow past your wall clock time.
Try setting a lower time limit to see if it completes, and like Professor
Case suggested, set ntpr=1, and nstlim=10.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu May 05 2011 - 07:00:02 PDT
