[gmx-users] RE: Bound oxygen molecule

[Gia Maisuradze]

Anton,

Thanks for your reply. Yes, it is probably better to create oxygenated heme 
building block in ff*.rtp file. Since I am going to do MD simulation and NMA 
for this system, I have realized that apart from ff*.rtp file I would 
probably need to add information in ff*.atp and ff*.itp files.

With best wishes,
Gia


----- Original Message ----- 
From: "Anton Feenstra" <feenstra at few.vu.nl>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, July 12, 2006 5:52 AM
Subject: Re: [gmx-users] RE: Bound oxygen molecule


> Gia Maisuradze wrote:
>> [...] Although the conversion was failed I
>> still got .itp files which do not include molecular oxygen. My question 
>> is following: should I change these itp files obtained after failure by 
>> adding information about bonds, angles, etc. for molecular oxygen  or go 
>> to the ffxxxbon.itp file and add bonds, angles, dihedrals for molecular 
>> oxygen and then perform the conversion?
>
> There are two ways to solve the conversion problem. One is to do what you 
> suggest: take the generated .top file and add the oxygen atoms, bonds, 
> angles, dihedrals, and impropers. The other is to create an oxygenated 
> heme building block in the ff*.rtp file. This would be similar (adding 
> atoms, bonds, angles, dih's and exclusions), but more general (i.e., if 
> you do it once, you can afterwards automatically convert oxygenated heme 
> systems).
>
> In both cases, however, you have to make decisions on the parameters, 
> i.e., atom types, charges, bond types, angle types, etc. You may be able 
> to make do with existing types, since you have some rather uncommon 
> combinations (like Fe-O bond, Fe-O-O and C-Fe-O angles, etc.) you will 
> probably have to add your 'own' types for some of them.
>
>> If anybody already have the topology for this case, I would appreciate to 
>> know what parameters (e.g. force constants) were used.
>
> No, sorry, no help there. You could have a look in other forcefields, or 
> publications, for which parameters people have used. Be aware that in 
> general you cannot simply mix parameters from different forcefields, but 
> using the examples may help you choose appropriate parameter values for 
> your forcefield.
>
>
> -- 
> Groetjes,
>
> Anton
>
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
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