Dear Case
Sorry for making you confuse. I am trying to make it more clear.
'Sometimes' means the structures yielded out in time scale, some
structures show that the whole molecule structure stay together, some
structures show that the molecule became two parts.
Because this molecule cannot be found in ff99 force field, I generate
top and crd files of the molecule using antechanber and GAFF force
field. Then the whole complex was made by tleap.
After this step, the top and crd files were input to run MD, and my MD
method is Glycam.
Yes, the covalent bonds in the molecule were broken in some structures
in the trajectory file.
Thanks
Jason
On 9/29/10, case <case.biomaps.rutgers.edu> wrote:
> 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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--
Yusheng Jason Jiang
Department of Chemistry
Georgia State University
Atlanta, 30302 GA
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Received on Wed Sep 29 2010 - 10:00:15 PDT
