[gmx-users] Re: phosphotyrosine

[David van der Spoel]

On Fri, 26 Apr 2002, Graham Smith wrote:

>[ SEP ]
>...
> [ dihedrals ]
>...
>   CB    OG     P   O1P     gd_9
>   CB    OG     P   O1P     gd_11
>
>is this correct? One of these has multiplicity 2, one 3. 
>So it would make sense if there's double bond character I guess. 
What you are doing here is adding two cosines to give you a slightly more
complicated function with the minimum at 180 and two less deep minima
close to 60 and -60 (but not exactly there). This potential is added to
the 1-4 interaction and together they should describe the rotation around
the OG-P bond. The 1-4 will make the 180 minimum even deeper with respect
to the other two. I can't judge whether this is correct, you would have to
do quantum calculations of the angle dependence of the energy.


>To use Hansson, Nordlund and Aqvist's parameters I had to introduce a new
>atom type OP. I let gromacs use the normal Cij = sqrt(Cii Cjj) combination
>rules for normal LJ, which was what Hansson et al did, but I seemed to
>need explicit combination rules for LJ-14 if I was not to get zeros, so I
>just used the same ones as for OA. Seem OK?
This seems incorrect. The 1-4 parameters should be generated automatically
if you specify LJ parameters in the atomtypes section. Check your tpr
file.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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