Date: Wed, 15 Jan 2020 11:44:40 +0100
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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>>
>>
>>
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(image/jpeg attachment: sugar_split.jpg)
