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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Received on Mon Jun 27 2011 - 11:00:04 PDT
