[gmx-users] Fwd: Assistance

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 30 09:14:08 CEST 2008


For such issues we have the gmx-users list. Please post questions
there (subscribe if you haven't already done so). Actually, you can
find the answer in the archives of this list. Flattery will bring you
nowhere (well, at least it will keep me gentle in my reply ;))
Advantages of the user list include: direct access to the combined
knowledge of all active participants on the list and archiving of
questions and answers for others to benefit from.


---------- Forwarded message ----------
From: willons999 <willons999 at 163.com>
Date: 2008/7/30
Subject: Assistance
To: tsjerkw at gmail.com

Dear Tsjerk
I'm a new gmx-user ,and simulating a P450 structure. I know you are an
expert in gmx.

I have a problem with pdb2gmx simulating a iron-sulfur bond. In the
pdb file heme-Fe atom is covalently bonded to Cys-S atom. However,
after pdb2gmx the Fe-S bond is broken and a new bond S-H is formed. Is
it possible to allow that bond Fe-S is not broken in pdb2gmx? And how?

Thank you very much!



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list