No we were talking about the parmed program included in AmberTools.
Do not do any processing before viewing the structure. Load into VMD the
prmtop used for the minimization or md, and then load into that molecule
the restart file using amber7 restart format in VMD. This will eliminate
possible problems in your fixatomorder command (I do not know what this is
doing).
On Wed, Jan 15, 2020, 8:52 AM MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
wrote:
> Ok, I think that I use parm...Can be this? Do you refer to this?:
>
>
> parm smp-199-mdk0rig.top
> trajin smp-199mdk0rig_vcon3.mdcrd
> fixatomorder outprefix reorder
> trajout reorder-smp-199mdk0_vcon3.nc
>
> I use this script to see the final structure by VMD
>
>
> Thanx in advance,
>
>
> Myriam
>
>
>
>
>
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>
> > 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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> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >>
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> >>
> >>
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Received on Wed Jan 15 2020 - 10:30:02 PST
