[gmx-users] Gromos Parameters for Heme bound Oxygen

[Justin A. Lemkul]

Olaniyi Yusuff wrote:
> Dear gmx users,
> I would like to know if any one has parameters for oxygen or 
> carbonmonoxide bound to the heme in hemoglobin.
> I am running MD simulations on hemoglobin using the gromos force field 
> G43a1 in gromacs, i had no problem when i used the pdb structure for 
> pure hemoglobin, but when i try to convert the pdb structure files for 
> the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was 
> complain of my oxy and carbomonoxy residue unknown i.e not defined in 
> the .rtp file.
> so i would like to know if there is anyone with parameters for these 
> kind of heme in gromacs or better still another reference of force field 
> with parameters for them that can be use in gromacs.
> 

If it has been published, then perhaps the authors of that particular study will 
share them with you.  If not, then realize what you are trying to do is 
certainly an expert topic, one that is not addressed easily:

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

-Justin

> Thanks
> 
> Kamil yusuff
> Deparment of Chemistry,
> University of Ibadan ,Nigeria.
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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