R: [gmx-users] About Zn paramter

[Spitaleri Andrea]

Hi there,

depending on which FF are you using, you may try ZAFF parameters in amber99sb:

http://pubs.acs.org/doi/abs/10.1021/ct1002626

Hope it helps

and




------------------------------------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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________________________________________
Da: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] per conto di Justin A. Lemkul [jalemkul at vt.edu]
Inviato: mercoledì 27 ottobre 2010 16.54
A: Discussion list for GROMACS users
Oggetto: Re: [gmx-users] About Zn paramter

babu gokul wrote:
> Dear all
> I am including the parameter for the Zinc in the topology file all the
> bonded and nonbonded parameters have been included in the topology still
> it is not accepting the parameter the Zn atom move away from the
> coordination.
>

Have you actually specified bonds between the Zn and its coordinating residues?
  Such a task is not trivial to define, and would likely require thorough
reparameterization of all species involved.  In any case, if there are actual
bonds, they cannot be broken.  If you are relying simply on nonbonded
interactions to hold Zn in place, this may not work and likely represents a
deficiency in the model.

If you can justify doing so (i.e., defend against reviewer criticism), then you
might be able to apply distance restraints to keep the position of Zn relatively
consistent.

Always keep in mind:
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

-Justin

> Thanking you in advance
>
> E R Azhagiya singam
>

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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