AMBER: surface area over the trajectory

From: mkseo <>
Date: Mon, 9 Jul 2007 15:52:32 -0600

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
The input that I used is:

Calculate Solvet Accessible Surface Area of Protein
    imin = 5,

To run this:
$AMBERHOME/exe/sander -O -i -p prmtop -y inptraj -o

However, I got the following error:
mdfil: Error unknown flag: -y

      usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r
                    [-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.


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