[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 [


IN di.pbd there is no CL atoms.
> NIlesh
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091117/f9abfd7d/attachment.html>

More information about the gromacs.org_gmx-users mailing list