Are the lengthened O-H bonds present in your PDB that you use to create your
prmtop file? If coordinates exist already, then tleap/sleap should just use
those coordinates when you create a topology and restart file.
Good luck!
Jason
On Sun, Dec 26, 2010 at 4:34 PM, case <case.biomaps.rutgers.edu> wrote:
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 26 2010 - 16:00:06 PST
