On Sun, Dec 26, 2010, leila karami wrote:
>
> I did simulation in gromacs. I converted gromacs trajrctory file (xtc) to
> amber trajectory file (mdcrd) by VMD
>
> 1) the length of O-H bonds are longer than those of normal waters. 2) there
> are new bonds between H atoms
1) is weird...can you double check? Are the coordinates of some water
molecule in the amber trajectory file different than those from gromacs?
Can you post a small example (i.e. just a single water molecule)?
As already pointed out, 2) is expected. If you don't want those bonds, you
can use the "set default FlexibleWater on" command in LEaP. But note that you
could not then use that prmtop file to do Amber simulations, just analysis.
....dac
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Received on Sun Dec 26 2010 - 16:00:05 PST
