[gmx-users] ffgmx2 can be used for non-protein molecules

[K.A. Feenstra]

Áõ ËÉ°Ø wrote:
> 
> hi, everyone:
> 
>      I want to add NOE distance restraints to a small molecule.
> In ffgmx forcefield I can't pinpoint hydrogens, but when
> I decide to select ffgmx2, there's "protein only" in the
> parentheses, so I'm wondering whether it's proper to use ffgmx2 for
> this small molecule-NON-protein!

Basically ffgmx and ffgmx2 are identical, the only difference being the
addition of non-charged non-Lennard-Jones hydrogen atoms, i.e. they are
bonded with a bond and angles, but otherwise have no interactions with
the system. But, since the conversion was done manually and is pretty
tedious, it was only done for amino acids (and a very few other things).
So, there is nothing inherently non-protein in ffgmx2, it is simply
the fact that only the protein-related stuff is included.

>      It seems to be one way to solve this problem that just use the
> ffgmx forcefield with building dummy atoms from vicinal
> heavy atoms to locate the hydrogens which are to be constrained.
> Does it make sense?

Yes, in principle using the ffgmx (or even better: the ffG43a) with
dummy atoms for the hydrogens is more sensible than using ffgmx2,
since that will create nicely virtual particles: other than having
a defined coordinate inside the protein, these hydrogens are not
really there, as far as the forcefield is concerned. But you'll 
have to add them by hand, or write a program/script that does it 
for you... 
I'm sure many other people would be interested in this, though!

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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