Hello Carlos,
If coordinates sets are read from trajectory, why are initial
coordinates (with -c option) needed?
Second question:
Should I define that how often ntwx, ntwe, ntwr, ntpr are saved in
input file?
I think that data should be saved for each frame of MD trajectory
automatically.
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.
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
>> > ===================================================================
>> >
>> ----------------------------------------------------------------------
>> -
>> > The AMBER Mail Reflector
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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 - 06:07:47 PDT
