On Mon, Jun 27, 2011 at 2:06 PM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> Hello,
> I am not sure that it is possible to perform SMD by pmemd. Try to use
> sander.MPI instead of pmemd.MPI.
>
SMD *does* work in pmemd via the NMROPT facility (not via the NCSU codes),
last I knew. (At least in Amber 11).
HTH,
Jason
>
> On Mon, Jun 27, 2011 at 9:49 PM, George Tzotzos <gtzotzos.me.com> wrote:
> > Hi everybody,
> >
> > I've just completed a 10ns production run of a protein-ligand complex. I
> would like to study the dissociation of this complex and fI thought that
> SMD would be suitable for this purpose. I tried to repeat the process
> described in the Amber 11 manual as well as in this website (
> http://enzyme.fbb.msu.ru/Tutorials/Tutorial_3/).
> >
> > I've started sander from a directory containing the solvated prmtop file,
> the trajectory from the production run and a distance restraint file.
> >
> > When I run
> >
> > mpirun -np 12 pmemd.MPI -O -i smd.in -o smd.out -p 2wc6_bom_solv.prmtop
> -c prod.rst -r smd.rst -x smd.mdcrd
> >
> > I get
> >
> > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> >
> > smd 2wc6-bombykol
> > &cntrl
> > imin=0,irest=1,ntx=5,
> > nstlim=500000,dt=0.002,
> > ntc=2,ntf=2,
> > cut=8.0, ntb=2, ntp=1, taup=2.0,
> > ntpr=1000, ntwx=1000, ntwr=5000,
> > ntt=3, gamma_ln=2.0, ig=-1,
> > temp0=300.0,
> > jar=1,
> > /
> > &wt TYPE='DUMPFREQ', istep1=1, /
> > &wt TYPE='END', /
> > DISANG=dist.RST
> > DUMPAVE=dist_vs_t
> > LISTIN=POUT
> > LISTOUT=POUT
> >
> > and the distance restraint dist.RST
> >
> > # Change distance restraint between atoms
> > &rst iat=1533,2223, r2=2.0, rk2=1.0725, r2a=8.0 /
> >
> > where 1533 and 2223 are atom numbers derived from the pdb file.
> >
> > Any help would be much appreciated.
> >
> > Regards
> >
> > George
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dmitry Nilov
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
> web: http://enzyme.fbb.msu.ru/
>
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> 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 Mon Jun 27 2011 - 17:00:05 PDT
