AMBER Archive (2009)

Subject: Re: [AMBER] Error in minimal

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 15 2009 - 06:56:02 CDT

On Tue, Sep 15, 2009, xuemeiwang1103 wrote:

> ifbox=2 in prmtop but angles are not correct

In brief: this indicates that the prmtop file was made with the solvateOct
command (so you have a truncated octahedron), but that the coordinates do
*not* seem to be for a truncated octahedron.

We need information about what LEaP commands you used to solvate your system.
This error probably has nothing to do with changes you made to the pdb file.

A couple of quick points:

1. double-check that the input coordinate file is exactly the one created at
the same time as the prmtop file you are using.

2. look at the final line of the input coordinate file, and let us know what
is there.

....dac

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