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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Received on Wed Jan 15 2020 - 05:00:02 PST
