Dear Dr. case,
Thank you. As you pointed out, the problem was with re-imaging.
I used the command -----> ptraj solvated-complex.prmtop < ptraj.in
ptraj.in previoulsly was
trajin heat.mdcrd
trajin density.mdcrd
trajin equil.mdcrd
trajin prod1.mdcrd
trajin prod2.mdcrd
trajin prod3.mdcrd
trajin prod4.mdcrd
trajout re-imaged.mdcrd
center :1-306
go
adding "image familiar" to this file solved the problem
Thank you
Regards,
On Wed, May 23, 2012 at 8:17 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 24 2012 - 00:00:02 PDT
