[AMBER] Corresponding dry trajectory and PDB

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Thu, 24 Apr 2014 03:45:21 -0700

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. 

-- 
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Apr 24 2014 - 04:00:03 PDT
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