VMD-L Mailing List

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Wed Dec 01 2010 - 13:45:25 CST

Ok! I meant, one could make a selection according to the system you have..

If its the DNA, you make a selection for DNA
eg: pbc unwrap -sel "nucleic"

or, make a selection for protein and DNA
pbc unwrap -sel "protein and nucleic"

Look up the pbcTools user guide for more help

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Ramya

On Wed, Dec 1, 2010 at 1:27 PM, Buddhadev Maiti <chebm_at_langate.gsu.edu>wrote:

> Dear Ramya,
>
> thank you for your suggestions. I tried to use the pbc command but
> unfortunately I had no success.
> In my trajectory the DNA jumps away from the protein due to wrapping
> problems. When I use the
> command pbc unwrap -sel "protein", this problem is not corrected.
>
> I then tried to use pbc join -now I got an error message saying that the
> command is unknown.
> I also tried to use the commands
>
> pbc join compound -first 0 -last 0
> pbc unwrap
>
> because in my first frame the DNA and protein still interact. Unfortunately
> I have not understood how the
> "compound" has to be practically specified. Could you please give me a few
> examples ?
>
> Thanks for your help and have a nice day,
>
> Maiti
>
>
>
> >>> Ramya Gamini <ramyabhargavi_at_gmail.com> 12/01/10 12:37 PM >>>
> Hi Buddhadev,
>
> Use the PBCTools plugin
> You can do post processing using the pbc unwrap command:
>
>
> Load the entire trajectory, and make sure you are at the first frame
>
> on TkConsole type,
>
> pbc unwrap -sel "protein"
>
>
> Hope it helps,
> Ramya
>
> On Mon, Nov 29, 2010 at 1:41 PM, Buddhadev Maiti <chebm_at_langate.gsu.edu
> >wrote:
>
> > Dear NAMD users,
> >
> > I recently ran some NPT simulations on a very large system composed by
> > different subunits.
> > What happens is that sometimes a part of the system comes out of the
> water
> > box so that
> > due to the wrapping procedure, one of the subunits is reflected on the
> > opposite side of the box.
> > Obviously in my following simulations I disabled the wrapping command and
> I
> > also used a larger
> > water box. However, I don't want to waste my old work, so I was wondering
> > if there is any
> > post-processing of the trajectory that I can use to fix the problem.
> >
> > So far I tried to address the problem using ptraj. here is my script:
> >
> > trajin file-in.dcd
> > trajout file-out.dcd CHARMM
> > center :1-9854 mass origin
> > image origin center
> >
> > However this script does not always work. Sometimes I have to use an
> > alternative script:
> >
> > trajin file-in.dcd
> > trajout file-out.dcd CHARMM
> > center :1-9854 mass origin
> >
> > Unfortunately, there are situations when neither of these scripts work.
> > The simulations I am tryiong to analyze have all been performed in the
> > same way, so there is no general rule that I could figure out as to when
> > one script is more suitable than the other. Can anyone help me ?
> > Is there any reliable post-processing strategy to correct the wrapping
> > problems ?
> >
> > Thanks for your help,
> >
> > Maiti
> >
> >
> >
>
>