Superb. Thanks jason
On Thu, Apr 24, 2014 at 1:32 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, 2014-04-24 at 03:45 -0700, Soumendranath Bhakat wrote:
> > Dear Amberists;
> >
> > Just a query
> >
> > I ams stripping water and counter ions from a trajectory
> >
> > trajin md100.mdcrd
> > center :1-154
> > image center familiar
> > strip :WAT
> > strip :Cl-
> > trajout wt1mg_dry.crd
> > go
> >
> > I think to generate a corresponding PDB for MD to visualise the
> trajectory
> > the input is
> >
> > trajin md100.mdcrd
> > trajout stripped_pdb.pdb
> > strip :WAT
> > strip :Cl-
> >
> >
> > To generate correponding .top file I think I need to process in tleap
> like
> > that
> >
> > mol = loadpdb strip_pdb.pdb
> > saveAmberParm mol strip_pdb.top strip_pdb.rst
> > quit
> >
> >
> > I think I am going right. I found that sometimes during visualisation the
> > corresponding PDB and topology creates problem which has been highlighted
> > in this thread http://archive.ambermd.org/201201/0192.html
> >
> > Please confirm me if I am going in a right direction or not as it is
> > crucial for visualisation of the trajectory.
>
> There is an easier way to do this now with cpptraj, and you can generate
> a topology file for visualization in the same step:
>
> trajin md100.mdcrd
> autoimage
> strip :WAT,Cl- outprefix stripped
> trajout wt1mg_dry.mdcrd
>
>
> This does basically the same thing your first script did (only a little
> more reliably). The "outprefix" command will create a new topology file
> called stripped_<original.prmtop> where <original.prmtop> is the
> original topology file you used.
>
> There is no need to go back through tleap.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Apr 24 2014 - 05:30:04 PDT
