Hello,
I am not sure that it is possible to perform SMD by pmemd. Try to use
sander.MPI instead of pmemd.MPI.
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
>
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>
--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
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Received on Mon Jun 27 2011 - 13:30:04 PDT
