This is my "modified" input file for minimization:
initial minimisation of our structure
&cntrl
imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=6, ntb=0
/
This is the "modified" code that I typed in for minimization
$AMBERHOME/exe/sander -O -i min_kelly.in -o min_kelly.out -p
kelly.prmtop -c kelly.inpcrd -r min_kelly.rst
But the restart (.rst) file is still not created. Can anyone help me please?
Thanks in advance
Su.
On 9/25/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> what does sander say in the output file from the minimization?
> note that igb=0 does not mean "no solvent", it sets a periodic
> system. you might try igb=6.
>
>
> On 9/25/07, Su Nwe <snwe001.gmail.com> wrote:
> > Dear Amber users
> >
> > I'm trying to run a simple molecular dynamic "without solvent" on an
> > organic molecule using Amber 9. I could neither do minimization nor
> > molecular dynamics. I'm assuming that I made some errors in setting
> > parameters.
> >
> > The following is my minimization input file.
> > initial minimisation
> > &cntrl
> > imin=1, maxcyc=2000, ntr=0, ntpr=5, ntmin=0, igb=0
> > /
> >
> > After minimization, .rst file wasn't created.
> >
> > This is my molecular dynamic input file.
> > 300K constant temp MD
> > &cntrl
> > imin=0, ntb=1,
> > ntc=2, ntf=2,
> > tempi=300.0, temp0=300.0,
> > ntt=3, gamma_ln=1.0,
> > nstlim=1000, dt=0.002,
> > ntpr=1, ntwx=1,
> > /
> >
> > I tried running the system "with solvent". Both minimization and
> > molecular dynamic works, but when I looked at the molecule (.mdcrd
> > file) using VMD, the molecules were shooting out everywhere and moving
> > so randomly.
> >
> > Can someone please help me figure out what I'm doing wrong or give me
> > some comment on my input files.
> >
> > Thanks in advance
> >
> > Sincerely,
> > Su.
> >
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>
>
>
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Received on Wed Sep 26 2007 - 06:07:26 PDT
