AMBER Archive (2007)

Subject: Re: AMBER: Minimization and MD input files

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 25 2007 - 15:34:14 CDT

my guess is that the -i is being interpreted as your output file
since it is right after -o, and then the min_kelly.in is what it thinks is
the next flag. You probably mean to say "sander -O" with a capital
letter O rather than lower case.

On 9/25/07, Su Nwe <snwe001_at_gmail.com> wrote:
>
> Thanks you all for answering my questions.
>
>
> This is the code I typed in for minization:
> $AMBERHOME/exe/sander -o -i min_kelly.in -o min_kelly.out -p
> kelly.prmtop -c kelly.inpcrd -r min_kelly.rst
>
> I added igb=6 and ntb=0 to my input file. ... (Thanks to David C. and
> Carlos S :)
>
> This is the error message I got (printed to terminal):
> mdfil: Error unknown flag: min_kelly.in
>
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
> -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
> mdinfo -radii radii]
> Consult the manual for additional options.
>
> Mr. Walker: I do not understand what you mean by this.
> "How exactly are you running the minimizations - interactively or through
> a
> queuing system?"
>
>
> And I forgot to mention this: I'm running Amber 9 on Mac OS X 10.4.10
>
> On 9/25/07, David A. Case <case_at_scripps.edu> wrote:
> > On Tue, Sep 25, 2007, Su Nwe wrote:
> > >
> > > 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
> > > /
> >
> > The default in sander is ntb=1, that is, for a periodic box with
> solvent.
> > If you want a simulation "without solvent", you need to specific ntb=0.
> >
> > >
> > > 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.
> >
> > This sounds correct: if you want the animation to look "nice" (with all
> the
> > molecules in the central unit cell,) you need to use the "image" command
> in
> > ptraj to re-pack everything into the central unit cell.
> >
> > These may not be the only problems, but I hope they will get you going
> in the
> > proper direction.
> >
> > ....dac
> >
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