[gmx-users] pdb2gmx : treat CL as C

[Manik Mayur]

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
> --
> 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>