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

From: case <>
Date: Mon, 27 Dec 2010 09:02:52 -0500

On Sun, Dec 26, 2010, Bill Ross wrote:

> > If coordinates exist already, then tleap/sleap should just use
> > those coordinates when you create a topology and restart file.
> Leap will not determine the O-H bond length from the gromacs
> trajectory. And if you ran the prmtop/inpcrd in sander or pmemd,
> the length should immediately go to what the bond spec is for OW-HW
> in the parm.dat file, no matter what it started out as in the pdb.

Just to amplify a bit: If you run a *simulation* (with sander/pmemd) and shake
turned on, then the bond lengths will be reset to the target values in the
prmtop file.

If (as I suspect) all you wish to do is analyze the existing trajectory, then
the coordinates should not be changing from what they were originally. If
they are, then something should be fixed, but note that the conversion program
you are using was written by others.


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Received on Mon Dec 27 2010 - 06:30:03 PST
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