On 7/10/07, Mikyung <seo.ualberta.ca> wrote:
> Hello Carlos,
>
> If coordinates sets are read from trajectory, why are initial
> coordinates (with -c option) needed?
no reason other than minimal changes to the code this way.
>
> Second question:
> Should I define that how often ntwx, ntwe, ntwr, ntpr are saved in
> input file?
these should not matter
> I think that data should be saved for each frame of MD trajectory
> automatically.
yes, but your output might depend on how many steps you minimize
>
> Third question:
> I ran job with the following command but I don't get any output in
> *.out file even though ntwx=1, ntwe=1, ntwr=1 and ntpr=1 in input file
> to calculate surface area.
>
that's odd, does everything work ok if you use imin=1 and otherwise the
same files? (make sure to only be using a copy of the trajectory you
want to analyze!)
> sander -O -i surface.in -o surface.out -p topology.top -c initial.crd
> -x MDtraj.crd
>
>
> Thanks
>
>
>
> On 10-Jul-07, at 4:33 AM, Carlos Simmerling wrote:
>
> > 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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> >> >
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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
> > ===================================================================
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
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Received on Wed Jul 11 2007 - 06:07:49 PDT
