Hi,
Can you send me off-list the topology and a few frames that I can use
to reproduce your issue? Thanks,
-Dan
On Mon, Mar 4, 2019 at 3:38 AM zaid kamal <z.kamal.rediffmail.com> wrote:
>
> Thank you, David, for your response. I have used the following commands:
>
> trajin zkm.mdcrd
>
> autoimage
>
> strip :WAT
>
> strip :Cl-
>
> trajout zkm-dry.mdcrd nobox
>
>
>
> I have also used iwrap=1 during the simulation run. When auto-image did not work worked, I used
>
> following
>
> too:
>
> 1. center :1-100 mass origin (including ligand)
>
> image origin center familiar
>
> 2. center :100 (ligand only)
>
> image center familiar
>
> Please let me know if I have done it correctly or not.
>
> Thanks,
>
> Zaid
>
>
>
> >On Fri, Mar 01, 2019, zaid kamal wrote:
>
> >
>
> >I have used Amber18 and being a beginner, I am facing a problem in
>
> >autoimaging the ligand along with the protein. In autoimage command
>
> >only the protein is imaged and ligand dissociates far away at different
>
> >directions. When i tried to center my ligand, then the protein
>
> >fluctuates.
>
>
>
> It's pretty unusual, but far from impossible, for autoimage to fail.
>
> Can you say exactly what commands you used? If you haven't done so yet,
>
> be sure to try "autoimage" with no arguments and no other centering
>
> commands.
>
>
>
> ....dac
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Received on Mon Mar 04 2019 - 12:30:02 PST
