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

[Songbai Liu]

Groeten 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!

>     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.

                        O
                        |
C=C-C         O   O     C=O
|   "         "   "     |
C=C-C-C-C-C-C-p-C-C---N-c-C
              |       |   |
              O   O   C---c-C-C-C
              |   "         |   |
              c-O-C-C-C     C-C-C
              |
            C-C
              |
              C
I don't know if what I had said makes sense.

Best Regards,
Songbai Liu
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