Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules

From: case <>
Date: Mon, 27 Dec 2010 09:12:43 -0500

On Mon, Dec 27, 2010, leila karami wrote:
> length of the OW-HW bond relating to a special water molecule in a certain
> time is 4.9 nm and 0.1 nm
> in amber and gromacs, respectively.I calculated these distances by g_bond in
> gromacs and ptraj (distance) in amber.

This error reporting thread is not going anywhere useful. We would need to
know *exactly* what steps you took (from the very beginning); and, you will
need to examine by hand the coordinates in the mdcrd file (and in the original
gromacs file) of this key water molecule.

A 49 Ang. bond sounds a bit like an imaging problem: does your simulation box
have a side that is close to 49 Ang?


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Received on Mon Dec 27 2010 - 06:30:04 PST
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