AMBER Archive (2007)

Subject: Re: AMBER: surface area over the trajectory

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jul 09 2007 - 17:30:54 CDT

specify the input trajectory with -x, not -y.

On 7/9/07, mkseo <seo_at_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_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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