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
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
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