On Wed, Sep 29, 2010, Jiang Yusheng wrote:
> >> I am running Glycam MD. I found the ligand in the complex separated
> >> into two parts sometimes.
>
> This molecule is in the crystal structure, so I didn't modify anything
> from it. But I used GAFF and antechanber generate its topology and
> coordinate files since leaprc.FF99 doesn't include this molecule.
This problem report is somewhat confusing. You say alternately that you are
using glycam and antechamber. Also the phrase "ligand in the complex
separated into two parts sometimes" is very vague...what exactly is happening?
Does the simulation seem to be breaking covalent bonds? What do you mean by
"sometimes"?
I suspect that we would need to know a *lot* more about what you have really
done to have any hope of offering real help.
[As a wild guess: could this be an imaging problem? Have you used the image
command in ptraj to bring everything back to the primary unit cell?]
....dac
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Received on Wed Sep 29 2010 - 08:00:08 PDT
