AMBER Archive (2004)

Subject: AMBER: Group in sander

From: Chris Moth (
Date: Mon Apr 12 2004 - 14:20:37 CDT

At 02:05 PM 4/12/2004, you wrote:
>Hi, I am using SANDER to minimize the energy of DNA before I calculate its
>frequencies using NMODE. Because I do not want to restrain any atoms in
>the mimization, so there is no group information in my input file for
>sander. However, I got an error message ", Group is not found
>at the end of file". Is the group information required for any
>minimization in sander? Thank you!

Make sure you do not have nmropt=1 or other group requiring option.

In case it might help, here is a valid minimization input file for sander
that does not have a group. (It was generated by MM_PBSA - so the options
are of course very different from what you will want to use).

File generated by Using MM GB MS
   ntf = 1, ntb = 0, dielc = 1,
   idecomp= 0,
   igb = 1, saltcon= 0.2,
   offset = 0.09, extdiel= 78.5,
   gbsa = 1, surften= 1.0,
   cut = 99999.0, nsnb = 99999,
   scnb = 2.0, scee = 1.2,

   imin = 1, maxcyc = 1, ncyc = 0,

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