[gmx-users] RE: Bound oxygen molecule

Anton Feenstra feenstra at few.vu.nl
Wed Jul 12 14:52:20 CEST 2006

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.



  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
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