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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Received on Thu Apr 24 2014 - 05:00:02 PDT
