[gmx-users] pdb2gmx : treat CL as C

Manik Mayur manik.mayur at gmail.com
Tue Nov 17 06:20:33 CET 2009


2009/11/17 Nilesh Dhumal <ndhumal at andrew.cmu.edu>

> this is the command,
>
> pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
>
> Here I have attached the dioxin.pdb file.
>

Check your dioxing.pdb.. there might be formatting issues. It might happen
the due to bad format of the pdb file, your 'L' is somehow removed from
'CL'. Follow the file format on pdb's website [
http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp#pdb]

-Manik

IN di.pbd there is no CL atoms.
> NIlesh
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