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

[David van der Spoel]

On Mon, 2002-09-30 at 04:50, 刘 松柏 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.
Songbai Liu




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Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
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spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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