On Thu, Jun 28, 2012 at 3:09 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> Hello. Thank you for the reply. In fact, a time step of 1fs seems to
> work around the problem. At the same time as i was writing the last
> email, I had submitted a job with dt = 0.001 and it finished without
> any problems. I havenŽt tested yet with pmemd.cuda, but IŽll do that
> later on.
> The two atoms involved in this case are O and H of the hydroxyl
> residue linked to the zinc atom of the active site. Where do I find
> the Lennard-Jones rmin values for them? The hole active site was
> parameterized following the steps on the MTK++ manual.
> IŽll follow your instructions as to getting a restart file from a
> previous step and test it out. IŽll inform you as soon as I have the
> results.
>
You can use xparmed.py to look at the lennard jones parameters. (Or, if
you want to use the ptraj-like, text-based version instead of the
point-and-click GUI, use parmed.py).
printDetails is the command that will give you the atomic details of every
atom given in your input mask.
Conveniently, ParmEd also has the ability to change the Lennard Jones
parameters for a single type. You can use changeLJSingleType to change the
lennard jones parameters of a single atom type.
As a note of caution, see the "printLJTypes" function, which will list all
atoms that share the same lennard jones type index with a given input mask.
If you don't want to change the LJ parameters of every atom in with that
index, you will need to use the command "addLJType" to segregate a subset
of that collection into a separate type that you can manipulate
independently.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 28 2012 - 14:00:04 PDT
