[gmx-users] ffgmx2 can be used for non-protein molecules
liulannet at hotmail.com
Tue Oct 1 06:45:58 CEST 2002
> 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
> 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?
>>You didn't say what your small molecule is, but >>try the OPLS force field
>>instead. It is all atom too, and in principle >>it is easier to find
>>parameters, since many function groups have >>already been parameterized.
This is the structure of the small molecule.
C=C-C O O C=O
| " " " |
| | |
O O C---c-C-C-C
| " | |
I don't know if what I had said makes sense.
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