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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Received on Wed Jul 11 2007 - 06:07:35 PDT
