On Wed, May 23, 2012, kamlesh sahu wrote:
>
> I am simulating a complex of two proteins and two ligands. After two
> nanoseconds of simulations when I see the re-imaged trajectories on vmd, I
> found that the water molecules moved away from solute and there seems no
> box. This was the script that I used to make prmtop and inpcrd files. Could
> you please tell me if there was a mistake. I am using amber10.
It sounds like the problem is with how you are doing the imaging. You
generally need to center the all the proteins and ligands using a mask, then
image. See the example under the "image" command in the ptraj chapter of the
AmberTools manual.
....dac
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Received on Wed May 23 2012 - 04:30:05 PDT
