Re: [AMBER] system imaging

From: InSuk Joung <i.joung.gmail.com>
Date: Tue, 10 May 2011 12:49:38 -0400

Hi,
Try the following two step processing:

#### first ptraj run ####
trajin tic_md_1.mdcrd 1 10000
unwrap :1-436
image center :* familiar com :1-436
trajout temp.mdcrd

#### second ptraj run ####
reference tic.rst7
trajin temp.mdcrd 1 10000 200
rms reference out tic_md_rmsd_new.dat .CA,C,N


On Tue, May 10, 2011 at 12:09 PM, Alex Rodriguez <alexdepremia.gmail.com>wrote:

> Hello everybody,
>
> I'm having what seems to be a system imaging problem, and I'm not able to
> solve it.
>
> I'm performing a pretty long trajectory (70 ns) on a protein dimer with two
> non-protein substrates (4 solute molecules). I performed it with PME in a
> cubic box and with iwrap=1.
>
> The question, is that when performing the rmsd analysis, it leads to
> unrealistic results. As recommended in the list, I tried to center the
> image. The ptraj script that I employed is:
>
> reference tic.rst7
> trajin tic_md_1.mdcrd 1 10000 200
> center :1-217 mass origin
> image origin center
> center :1-434 mass origin
> image origin center
> center :1-435 mass
> image origin center
> center :1-436 mass
> image origin center
> rms reference out tic_md_rmsd_new.dat .CA,C,N
>
> And the output is attached.
>
> Any suggestion?
>
> Thanks in advance
>
> Alex
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>


-- 
Best,
InSuk Joung
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 10 2011 - 10:00:05 PDT
Custom Search