The follow Dave's advi e and use parmed. Printbonds should be what you
want.
https://parmed.github.io/ParmEd/html/parmed.html
On Wed, Jan 15, 2020, 6:44 AM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:
> Yes, I use coordinates (.mdcrd or .crd) and prmtop in the VMD. I have
> attach a photo with the result of my tetrasaccharide.
> it's the first time that happens to me...
>
> Myriam
>
> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>
> > 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 - 03:30:02 PST
