Just one quick thing to check - how are you visualizing the ligand? Are you
using coordinates and prmtop (such as in Vmd) or are you allowing the viz
software to determine bonds? The latter might not reliably represent the
bonds used in md. How far apart do the ligand pieces move?
On Wed, Jan 15, 2020, 6:26 AM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:
> I have visualized the structure in the heat step, and my molecule is
> broken, so in effect, the problem is in minimization step. But, this
> phase doesn't create min.mdcrd file...
>
> "use parmed to check the prmtop file for the presence/absence of bonds
> between the parts of the ligand that are no longer together"
>
> How I do this?
>
> Thanx in advance
>
>
> Myriam
>
> David Case <david.case.rutgers.edu> escribió:
>
> > On Tue, Jan 14, 2020, MYRIAN TORRES RICO wrote:
> >>
> >>
> >> I'm looking for any idea about a problem with my results. I have
> >> launched a molecular dynamic of my complex ligand-protein (my ligand
> >> is a tetrasaccharide), and when finished all steps (minimization,
> >> heat, pressure and volume), my molecule is split.
> >
> > I'm guessing this means that some bond is missing in the carbohydrate
> > part. You'll probably see what is happening even after the minimization
> > step. Visualize the minimized structure and see which bonds are
> > "broken"; use parmed to check the prmtop file for the presence/absence
> > of bonds between the parts of the ligand that are no longer "together".
> >
> > Then, you will need to figure out what went wrong. It's a good idea to
> > set up just the ligand, and run a minimization on it. That gives you a
> > lot fewer things to look at.
> >
> > ....dac
> >
> >
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Received on Wed Jan 15 2020 - 03:00:02 PST
