Hi Ilyas,
I'm trying to do both minimization and MD. I'm trying to do this in explicit
solvent (water), because the protein is solvated under normal conditions.
Thus, the minimization is done to try and compact the water molecules and
get rid of air bubbles. I'm not sure if that is what I am actually
accomplishing, but that is the general idea.
Since I will be doing MD, how do I set those restraints? Regarding the
disulfide bond, that was fixed by changing the CYS residues to CYX, so that
error was resolved.
Thanks,
Melanie
PS. Sorry about the name confusion there; my coworker was helping me send my
emails, and accidentally signed her name in her hurry.
On Mon, Apr 4, 2011 at 7:23 AM, Ilyas Yildirim
<i-yildirim.northwestern.edu>wrote:
> Hi Audrey -
>
> What kind of calculation do you want to do on this structure? Just a
> minimization or MD? It is really difficult to find the best parameter set
> from analogy, but I would guess that it will not make a too big difference
> for this structure. Generally, minimization is done to get rid of close
> contacts. When I minimize nucleic acids in gas phase, for instance, I will
> see some distortions on the planes but they will vanishe in an MD run. The
> same thing would probably happen in your case. Also, how do you minimize the
> structure? In vacuum or using implicit solvent model? You might want to try
> to minimize the structure using one of the implicit solvent models
> implemented in AMBER if you did not try already. That might resemble the
> real environment more than gas phase.
>
> If the aim of the minimization is to prepare the best coordinates for the
> MD simulations, you might want to put some restraints on the structure (this
> can be positional and/or NMR distance/angle/torsional restraints).
>
> Another thing - I do not see any parameters defined for the sulphur region
> in the frcmod file (resid 1 and 9). After creating the bonds did leap give
> any error message for that sulphur bond?
>
>
> Best regards,
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~yildirim/ =
> -----------------------------------------------------------
>
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Received on Mon Apr 04 2011 - 20:00:02 PDT
