AMBER Archive (2007)

Subject: AMBER: surface area over the trajectory

From: mkseo (seo_at_ualberta.ca)
Date: Mon Jul 09 2007 - 16:52:32 CDT

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

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