yes
On 7/9/07, mkseo <seo.ualberta.ca> wrote:
> Should I also use "-c inpcrd" even though trajectory is read?
> Coordinates sets are read from trajectory, aren't they?
>
>
>
> On 9-Jul-07, at 4:30 PM, Carlos Simmerling wrote:
>
> > specify the input trajectory with -x, not -y.
> >
> >
> > On 7/9/07, mkseo <seo.ualberta.ca> wrote:
> >> Hello Amber users,
> >>
> >> I am trying to calculate solvent accessible surface area over a
> >> trajectory using AMBER 9.0.
> >> First, I loaded the trajectory file from MD simulations and used gbsa
> >> =2.
> >> The input that I used is:
> >>
> >> Calculate Solvet Accessible Surface Area of Protein
> >> &cntrl
> >> imin = 5,
> >> gbsa=2,
> >> surften=1
> >> /
> >>
> >> To run this:
> >> $AMBERHOME/exe/sander -O -i surface.in -p prmtop -y inptraj -o
> >> surface.out
> >>
> >> However, I got the following error:
> >> ----------------------------------------------------------------------
> >> --
> >> ----------------------------------------------------------------------
> >> --
> >> -----------------------------------------------------------
> >> mdfil: Error unknown flag: -y
> >>
> >> 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.
> >> ----------------------------------------------------------------------
> >> --
> >> ----------------------------------------------------------------------
> >> --
> >> ------------------------------------------------------------
> >>
> >> When I check the manual, "-y" option can be used.
> >> Can any one help me to solve this problem?
> >>
> >> Thanks in advance.
> >>
> >> Mikyung
> >
> >
> > --
> > ===================================================================
> > Carlos L. Simmerling, Ph.D.
> > Associate Professor Phone: (631) 632-1336
> > Center for Structural Biology Fax: (631) 632-1555
> > CMM Bldg, Room G80
> > Stony Brook University E-mail: carlos.simmerling.gmail.com
> > Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> > ===================================================================
> > -----------------------------------------------------------------------
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> > To post, send mail to amber.scripps.edu
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> >
>
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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Received on Wed Jul 11 2007 - 06:07:43 PDT
