[gmx-users] pdb2gmx showing error for FE in protein

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Jan 19 10:34:14 CET 2006


Which FF do you use?
In case of OPLSAA Fe2+ is included (watch the hint in the oplsaanb.itp).
Its also listed in the RTP-File. But beware, it should be written FE, 
not Fe.
So Pdb2gmx should recognize it...at least in GROMACS3.3.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

raja wrote:
> Dear gmxions,
>           The protein of my interst having Fe2+ in its active site,
>           while I try to use pdb2gmx , it shows error for the presense
>           of FE , but when I try for Zn it works. How do you peoples
>           treat these proteins with Fe in its active site.
> Kindly help me.
> with regards,
> B.Nataraj

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