On Fri, 2014-02-28 at 15:40 +0800, Changqing Yan wrote:
> Dear,
>
> I want to run a thermodynamical integration calculation. input file and
> script are like this:
>
> Initial minimisation of protein side chains and ions
> &cntrl
> imin=0, irest=1, ntx=5,
> cut=10, ntb=2, ntr=0,
> pres0=1.0, ntp=1, taup=2.0,
> ntc=2, ntf=2,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=1.0,
> nstlim=5000000, dt=0.001,
> ntpr=5000, ntwx=5000, ntwr=50000,
> icfe=1, clambda=0.0
> /
>
> pbs_mpirun $AMBERHOME/bin/sander.MPI -O -i ligand-md2.in -o
> ligand-md2-1.out -p complex-sol.prmtop -c ligand-md1.rst -r
> ligand-md2-1.rst -x ligand-md2-1.mdcrd -ref ligand-md1.rst
This command is not right for TI calculations. TI calculations with
sander requires a groupfile and a multisander approach.
> how can I fix this?
Work through the TI tutorial first:
http://ambermd.org/tutorials/advanced/tutorial6/
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 28 2014 - 05:30:03 PST
